Ben Bolstad
| Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: devel |
| git_last_commit: d422a05 |
| git_last_commit_date: 2024-04-30 10:16:21 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-24 11:39 -0400 (Wed, 24 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4284 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 249/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.69.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BufferedMatrix |
| Version: 1.69.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BufferedMatrix.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BufferedMatrix_1.69.0.tar.gz |
| StartedAt: 2024-07-23 22:35:09 -0400 (Tue, 23 Jul 2024) |
| EndedAt: 2024-07-23 22:37:43 -0400 (Tue, 23 Jul 2024) |
| EllapsedTime: 154.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BufferedMatrix.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BufferedMatrix_1.69.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BufferedMatrix/DESCRIPTION' ... OK
* this is package 'BufferedMatrix' version '1.69.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BufferedMatrix' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) BufferedMatrix-class.Rd:209: Lost braces; missing escapes or markup?
209 | $x^{power}$ elementwise of the matrix
| ^
prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword
prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details
prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value
prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references
prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso
prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/BufferedMatrix/libs/x64/BufferedMatrix.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... NONE
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'Rcodetesting.R'
Running 'c_code_level_tests.R'
Running 'objectTesting.R'
Running 'rawCalltesting.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
'F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/00check.log'
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'BufferedMatrix' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function 'dbm_ReadOnlyMode':
doubleBufferedMatrix.c:1580:7: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses]
1580 | if (!(Matrix->readonly) & setting){
| ^~~~~~~~~~~~~~~~~~~
doubleBufferedMatrix.c: At top level:
doubleBufferedMatrix.c:3327:12: warning: 'sort_double' defined but not used [-Wunused-function]
3327 | static int sort_double(const double *a1,const double *a2){
| ^~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init_package.c -o init_package.o
gcc -shared -s -static-libgcc -o BufferedMatrix.dll tmp.def RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'rowMeans' in package 'BufferedMatrix'
Creating a new generic function for 'rowSums' in package 'BufferedMatrix'
Creating a new generic function for 'colMeans' in package 'BufferedMatrix'
Creating a new generic function for 'colSums' in package 'BufferedMatrix'
Creating a generic function for 'ncol' from package 'base' in package 'BufferedMatrix'
Creating a generic function for 'nrow' from package 'base' in package 'BufferedMatrix'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix", "BufferedMatrix", .libPaths());.C("dbm_c_tester",integer(1))
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
Adding Additional Column
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000
Reassigning values
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 3
Buffer Cols: 3
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Activating Row Buffer
In row mode: 1
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Squaring Last Column
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
5.000000 10.000000 15.000000 20.000000 25.000000 900.000000
Square rooting Last Row, then turing off Row Buffer
In row mode: 0
Checking on value that should be not be in column buffer2.236068
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
2.236068 3.162278 3.872983 4.472136 5.000000 30.000000
Single Indexing. Assign each value its square
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Resizing Buffers Smaller
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Activating Row Mode.
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
Activating ReadOnly Mode.
The results of assignment is: 0
Printing matrix reversed.
900.000000 625.000000 400.000000 225.000000 100.000000 25.000000
841.000000 576.000000 361.000000 196.000000 81.000000 16.000000
784.000000 529.000000 324.000000 169.000000 64.000000 9.000000
729.000000 484.000000 289.000000 144.000000 49.000000 -30.000000
676.000000 441.000000 256.000000 121.000000 -20.000000 -10.000000
[[1]]
[1] 0
>
> proc.time()
user system elapsed
0.23 0.20 1.00
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
>
> ### this is used to control how many repetitions in something below
> ### higher values result in more checks.
> nreps <-100 ##20000
>
>
> ## test creation and some simple assignments and subsetting operations
>
> ## first on single elements
> tmp <- createBufferedMatrix(1000,10)
>
> tmp[10,5]
[1] 0
> tmp[10,5] <- 10
> tmp[10,5]
[1] 10
> tmp[10,5] <- 12.445
> tmp[10,5]
[1] 12.445
>
>
>
> ## now testing accessing multiple elements
> tmp2 <- createBufferedMatrix(10,20)
>
>
> tmp2[3,1] <- 51.34
> tmp2[9,2] <- 9.87654
> tmp2[,1:2]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[,-(3:20)]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
> tmp2[-3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
> tmp2[2,1:3]
[,1] [,2] [,3]
[1,] 0 0 0
> tmp2[3:9,1:3]
[,1] [,2] [,3]
[1,] 51.34 0.00000 0
[2,] 0.00 0.00000 0
[3,] 0.00 0.00000 0
[4,] 0.00 0.00000 0
[5,] 0.00 0.00000 0
[6,] 0.00 0.00000 0
[7,] 0.00 9.87654 0
> tmp2[-4,-4]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[9,] 0 0 0 0 0 0
>
> ## now testing accessing/assigning multiple elements
> tmp3 <- createBufferedMatrix(10,10)
>
> for (i in 1:10){
+ for (j in 1:10){
+ tmp3[i,j] <- (j-1)*10 + i
+ }
+ }
>
> tmp3[2:4,2:4]
[,1] [,2] [,3]
[1,] 12 22 32
[2,] 13 23 33
[3,] 14 24 34
> tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 11 21 31 11 21 31 91 1 11 1 11 21 31
[2,] 12 22 32 12 22 32 92 2 12 2 12 22 32
[3,] 13 23 33 13 23 33 93 3 13 3 13 23 33
[4,] 14 24 34 14 24 34 94 4 14 4 14 24 34
[5,] 15 25 35 15 25 35 95 5 15 5 15 25 35
[6,] 16 26 36 16 26 36 96 6 16 6 16 26 36
[7,] 17 27 37 17 27 37 97 7 17 7 17 27 37
[8,] 18 28 38 18 28 38 98 8 18 8 18 28 38
[9,] 19 29 39 19 29 39 99 9 19 9 19 29 39
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 41 51 61 71 81 91 91 81 71 61 51 41
[2,] 42 52 62 72 82 92 92 82 72 62 52 42
[3,] 43 53 63 73 83 93 93 83 73 63 53 43
[4,] 44 54 64 74 84 94 94 84 74 64 54 44
[5,] 45 55 65 75 85 95 95 85 75 65 55 45
[6,] 46 56 66 76 86 96 96 86 76 66 56 46
[7,] 47 57 67 77 87 97 97 87 77 67 57 47
[8,] 48 58 68 78 88 98 98 88 78 68 58 48
[9,] 49 59 69 79 89 99 99 89 79 69 59 49
[,26] [,27] [,28] [,29]
[1,] 31 21 11 1
[2,] 32 22 12 2
[3,] 33 23 13 3
[4,] 34 24 14 4
[5,] 35 25 15 5
[6,] 36 26 16 6
[7,] 37 27 17 7
[8,] 38 28 18 8
[9,] 39 29 19 9
> tmp3[-c(1:5),-c(6:10)]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 26 36 46
[2,] 7 17 27 37 47
[3,] 8 18 28 38 48
[4,] 9 19 29 39 49
[5,] 10 20 30 40 50
>
> ## assignment of whole columns
> tmp3[,1] <- c(1:10*100.0)
> tmp3[,1:2] <- tmp3[,1:2]*100
> tmp3[,1:2] <- tmp3[,2:1]
> tmp3[,1:2]
[,1] [,2]
[1,] 1100 1e+04
[2,] 1200 2e+04
[3,] 1300 3e+04
[4,] 1400 4e+04
[5,] 1500 5e+04
[6,] 1600 6e+04
[7,] 1700 7e+04
[8,] 1800 8e+04
[9,] 1900 9e+04
[10,] 2000 1e+05
>
>
> tmp3[,-1] <- tmp3[,1:9]
> tmp3[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1100 1100 1e+04 21 31 41 51 61 71 81
[2,] 1200 1200 2e+04 22 32 42 52 62 72 82
[3,] 1300 1300 3e+04 23 33 43 53 63 73 83
[4,] 1400 1400 4e+04 24 34 44 54 64 74 84
[5,] 1500 1500 5e+04 25 35 45 55 65 75 85
[6,] 1600 1600 6e+04 26 36 46 56 66 76 86
[7,] 1700 1700 7e+04 27 37 47 57 67 77 87
[8,] 1800 1800 8e+04 28 38 48 58 68 78 88
[9,] 1900 1900 9e+04 29 39 49 59 69 79 89
[10,] 2000 2000 1e+05 30 40 50 60 70 80 90
>
> tmp3[,1:2] <- rep(1,10)
> tmp3[,1:2] <- rep(1,20)
> tmp3[,1:2] <- matrix(c(1:5),1,5)
>
> tmp3[,-c(1:8)] <- matrix(c(1:5),1,5)
>
> tmp3[1,] <- 1:10
> tmp3[1,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
> tmp3[-1,] <- c(1,2)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 2 1 2 1 2 1 2 1 2 1
[10,] 1 2 1 2 1 2 1 2 1 2
> tmp3[-c(1:8),] <- matrix(c(1:5),1,5)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 1 3 5 2 4 1 3 5 2 4
[10,] 2 4 1 3 5 2 4 1 3 5
>
>
> tmp3[1:2,1:2] <- 5555.04
> tmp3[-(1:2),1:2] <- 1234.56789
>
>
>
> ## testing accessors for the directory and prefix
> directory(tmp3)
[1] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests"
> prefix(tmp3)
[1] "BM"
>
> ## testing if we can remove these objects
> rm(tmp, tmp2, tmp3)
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 468463 25.1 1021760 54.6 633411 33.9
Vcells 853879 6.6 8388608 64.0 2003053 15.3
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Tue Jul 23 22:35:39 2024"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Tue Jul 23 22:35:42 2024"
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
>
>
> RowMode(tmp2)
<pointer: 0x000001a7606ff2f0>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Tue Jul 23 22:36:07 2024"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Tue Jul 23 22:36:16 2024"
>
> ColMode(tmp2)
<pointer: 0x000001a7606ff2f0>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.7136650 -2.459588094 -0.4084730 -1.4316115
[2,] -0.3136963 -0.003272146 -0.1880919 0.0547613
[3,] 0.6232098 -1.049043693 0.4957434 -1.2765429
[4,] 0.9529704 -0.080470828 -0.4125626 -2.7781983
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.7136650 2.459588094 0.4084730 1.4316115
[2,] 0.3136963 0.003272146 0.1880919 0.0547613
[3,] 0.6232098 1.049043693 0.4957434 1.2765429
[4,] 0.9529704 0.080470828 0.4125626 2.7781983
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 9.9856730 1.56830740 0.6391189 1.1964997
[2,] 0.5600860 0.05720267 0.4336956 0.2340113
[3,] 0.7894364 1.02422834 0.7040905 1.1298420
[4,] 0.9762020 0.28367380 0.6423104 1.6667928
>
> my.function <- function(x,power){
+ (x+5)^power
+ }
>
> ewApply(tmp5,my.function,power=2)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 224.57039 43.14266 31.79966 38.39661
[2,] 30.91456 25.57530 29.52505 27.39487
[3,] 33.51757 36.29133 32.53665 37.57496
[4,] 35.71499 27.91721 31.83567 44.44613
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x000001a7606ff830>
> exp(tmp5)
<pointer: 0x000001a7606ff830>
> log(tmp5,2)
<pointer: 0x000001a7606ff830>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 467.4139
> Min(tmp5)
[1] 53.21259
> mean(tmp5)
[1] 72.94877
> Sum(tmp5)
[1] 14589.75
> Var(tmp5)
[1] 871.2038
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 91.37489 66.88286 70.74339 69.31789 75.05987 71.57389 70.61991 70.76807
[9] 72.56894 70.57795
> rowSums(tmp5)
[1] 1827.498 1337.657 1414.868 1386.358 1501.197 1431.478 1412.398 1415.361
[9] 1451.379 1411.559
> rowVars(tmp5)
[1] 7959.92026 79.35170 77.97176 68.29678 116.13390 49.82193
[7] 85.15119 64.22496 76.14358 109.11298
> rowSd(tmp5)
[1] 89.218385 8.907957 8.830162 8.264187 10.776544 7.058465 9.227740
[8] 8.014047 8.726029 10.445716
> rowMax(tmp5)
[1] 467.41385 84.97475 91.50465 92.50879 94.67726 83.27381 85.35461
[8] 84.08468 87.67488 89.01180
> rowMin(tmp5)
[1] 56.11684 53.23163 56.73931 58.10601 53.21259 59.14291 57.71813 56.56741
[9] 54.78142 54.85374
>
> colMeans(tmp5)
[1] 110.26011 71.61922 69.92508 74.87689 68.93468 73.57567 67.84347
[8] 74.09425 72.54283 73.47490 73.76967 67.04530 68.10979 68.96433
[15] 75.70627 75.00139 67.48230 70.67156 67.95095 67.12667
> colSums(tmp5)
[1] 1102.6011 716.1922 699.2508 748.7689 689.3468 735.7567 678.4347
[8] 740.9425 725.4283 734.7490 737.6967 670.4530 681.0979 689.6433
[15] 757.0627 750.0139 674.8230 706.7156 679.5095 671.2667
> colVars(tmp5)
[1] 15791.80962 128.35450 69.51457 101.32563 95.27259 129.60576
[7] 61.70909 40.19900 63.50716 24.93359 116.20327 66.46043
[13] 84.94710 55.59353 125.50853 70.44164 124.51185 75.84042
[19] 92.95392 131.63139
> colSd(tmp5)
[1] 125.665467 11.329365 8.337540 10.066063 9.760768 11.384453
[7] 7.855513 6.340268 7.969138 4.993354 10.779762 8.152327
[13] 9.216675 7.456107 11.203059 8.392952 11.158488 8.708640
[19] 9.641262 11.473072
> colMax(tmp5)
[1] 467.41385 89.79580 85.29871 92.50879 85.35461 91.50465 78.61689
[8] 82.76007 82.48044 83.04653 91.09238 78.99579 83.27381 81.64449
[15] 94.18616 89.01180 87.67488 87.33700 84.57421 94.67726
> colMin(tmp5)
[1] 60.47642 53.23163 60.67143 57.01884 54.78142 59.96096 57.71813 65.72333
[9] 56.11684 66.41709 60.96445 56.73931 57.33560 59.14291 54.75524 65.64470
[17] 53.21259 58.90668 56.56741 54.85374
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] 91.37489 NA 70.74339 69.31789 75.05987 71.57389 70.61991 70.76807
[9] 72.56894 70.57795
> rowSums(tmp5)
[1] 1827.498 NA 1414.868 1386.358 1501.197 1431.478 1412.398 1415.361
[9] 1451.379 1411.559
> rowVars(tmp5)
[1] 7959.92026 69.53297 77.97176 68.29678 116.13390 49.82193
[7] 85.15119 64.22496 76.14358 109.11298
> rowSd(tmp5)
[1] 89.218385 8.338643 8.830162 8.264187 10.776544 7.058465 9.227740
[8] 8.014047 8.726029 10.445716
> rowMax(tmp5)
[1] 467.41385 NA 91.50465 92.50879 94.67726 83.27381 85.35461
[8] 84.08468 87.67488 89.01180
> rowMin(tmp5)
[1] 56.11684 NA 56.73931 58.10601 53.21259 59.14291 57.71813 56.56741
[9] 54.78142 54.85374
>
> colMeans(tmp5)
[1] 110.26011 71.61922 69.92508 74.87689 68.93468 73.57567 67.84347
[8] 74.09425 NA 73.47490 73.76967 67.04530 68.10979 68.96433
[15] 75.70627 75.00139 67.48230 70.67156 67.95095 67.12667
> colSums(tmp5)
[1] 1102.6011 716.1922 699.2508 748.7689 689.3468 735.7567 678.4347
[8] 740.9425 NA 734.7490 737.6967 670.4530 681.0979 689.6433
[15] 757.0627 750.0139 674.8230 706.7156 679.5095 671.2667
> colVars(tmp5)
[1] 15791.80962 128.35450 69.51457 101.32563 95.27259 129.60576
[7] 61.70909 40.19900 NA 24.93359 116.20327 66.46043
[13] 84.94710 55.59353 125.50853 70.44164 124.51185 75.84042
[19] 92.95392 131.63139
> colSd(tmp5)
[1] 125.665467 11.329365 8.337540 10.066063 9.760768 11.384453
[7] 7.855513 6.340268 NA 4.993354 10.779762 8.152327
[13] 9.216675 7.456107 11.203059 8.392952 11.158488 8.708640
[19] 9.641262 11.473072
> colMax(tmp5)
[1] 467.41385 89.79580 85.29871 92.50879 85.35461 91.50465 78.61689
[8] 82.76007 NA 83.04653 91.09238 78.99579 83.27381 81.64449
[15] 94.18616 89.01180 87.67488 87.33700 84.57421 94.67726
> colMin(tmp5)
[1] 60.47642 53.23163 60.67143 57.01884 54.78142 59.96096 57.71813 65.72333
[9] NA 66.41709 60.96445 56.73931 57.33560 59.14291 54.75524 65.64470
[17] 53.21259 58.90668 56.56741 54.85374
>
> Max(tmp5,na.rm=TRUE)
[1] 467.4139
> Min(tmp5,na.rm=TRUE)
[1] 53.21259
> mean(tmp5,na.rm=TRUE)
[1] 72.90087
> Sum(tmp5,na.rm=TRUE)
[1] 14507.27
> Var(tmp5,na.rm=TRUE)
[1] 875.1427
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.37489 66.06194 70.74339 69.31789 75.05987 71.57389 70.61991 70.76807
[9] 72.56894 70.57795
> rowSums(tmp5,na.rm=TRUE)
[1] 1827.498 1255.177 1414.868 1386.358 1501.197 1431.478 1412.398 1415.361
[9] 1451.379 1411.559
> rowVars(tmp5,na.rm=TRUE)
[1] 7959.92026 69.53297 77.97176 68.29678 116.13390 49.82193
[7] 85.15119 64.22496 76.14358 109.11298
> rowSd(tmp5,na.rm=TRUE)
[1] 89.218385 8.338643 8.830162 8.264187 10.776544 7.058465 9.227740
[8] 8.014047 8.726029 10.445716
> rowMax(tmp5,na.rm=TRUE)
[1] 467.41385 84.97475 91.50465 92.50879 94.67726 83.27381 85.35461
[8] 84.08468 87.67488 89.01180
> rowMin(tmp5,na.rm=TRUE)
[1] 56.11684 53.23163 56.73931 58.10601 53.21259 59.14291 57.71813 56.56741
[9] 54.78142 54.85374
>
> colMeans(tmp5,na.rm=TRUE)
[1] 110.26011 71.61922 69.92508 74.87689 68.93468 73.57567 67.84347
[8] 74.09425 71.43866 73.47490 73.76967 67.04530 68.10979 68.96433
[15] 75.70627 75.00139 67.48230 70.67156 67.95095 67.12667
> colSums(tmp5,na.rm=TRUE)
[1] 1102.6011 716.1922 699.2508 748.7689 689.3468 735.7567 678.4347
[8] 740.9425 642.9479 734.7490 737.6967 670.4530 681.0979 689.6433
[15] 757.0627 750.0139 674.8230 706.7156 679.5095 671.2667
> colVars(tmp5,na.rm=TRUE)
[1] 15791.80962 128.35450 69.51457 101.32563 95.27259 129.60576
[7] 61.70909 40.19900 57.72944 24.93359 116.20327 66.46043
[13] 84.94710 55.59353 125.50853 70.44164 124.51185 75.84042
[19] 92.95392 131.63139
> colSd(tmp5,na.rm=TRUE)
[1] 125.665467 11.329365 8.337540 10.066063 9.760768 11.384453
[7] 7.855513 6.340268 7.597989 4.993354 10.779762 8.152327
[13] 9.216675 7.456107 11.203059 8.392952 11.158488 8.708640
[19] 9.641262 11.473072
> colMax(tmp5,na.rm=TRUE)
[1] 467.41385 89.79580 85.29871 92.50879 85.35461 91.50465 78.61689
[8] 82.76007 81.73165 83.04653 91.09238 78.99579 83.27381 81.64449
[15] 94.18616 89.01180 87.67488 87.33700 84.57421 94.67726
> colMin(tmp5,na.rm=TRUE)
[1] 60.47642 53.23163 60.67143 57.01884 54.78142 59.96096 57.71813 65.72333
[9] 56.11684 66.41709 60.96445 56.73931 57.33560 59.14291 54.75524 65.64470
[17] 53.21259 58.90668 56.56741 54.85374
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.37489 NaN 70.74339 69.31789 75.05987 71.57389 70.61991 70.76807
[9] 72.56894 70.57795
> rowSums(tmp5,na.rm=TRUE)
[1] 1827.498 0.000 1414.868 1386.358 1501.197 1431.478 1412.398 1415.361
[9] 1451.379 1411.559
> rowVars(tmp5,na.rm=TRUE)
[1] 7959.92026 NA 77.97176 68.29678 116.13390 49.82193
[7] 85.15119 64.22496 76.14358 109.11298
> rowSd(tmp5,na.rm=TRUE)
[1] 89.218385 NA 8.830162 8.264187 10.776544 7.058465 9.227740
[8] 8.014047 8.726029 10.445716
> rowMax(tmp5,na.rm=TRUE)
[1] 467.41385 NA 91.50465 92.50879 94.67726 83.27381 85.35461
[8] 84.08468 87.67488 89.01180
> rowMin(tmp5,na.rm=TRUE)
[1] 56.11684 NA 56.73931 58.10601 53.21259 59.14291 57.71813 56.56741
[9] 54.78142 54.85374
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 115.36183 73.66228 70.86647 76.86112 68.51038 72.30911 67.44242
[8] 75.02436 NaN 73.65539 73.17029 67.94990 68.68314 69.86679
[15] 78.03416 75.52797 68.04676 70.54260 67.58276 67.91872
> colSums(tmp5,na.rm=TRUE)
[1] 1038.2565 662.9605 637.7982 691.7501 616.5934 650.7820 606.9818
[8] 675.2192 0.0000 662.8985 658.5326 611.5491 618.1483 628.8011
[15] 702.3074 679.7517 612.4208 634.8834 608.2448 611.2685
> colVars(tmp5,na.rm=TRUE)
[1] 17472.97551 97.44003 68.23386 69.69828 105.15632 127.75940
[7] 67.61323 35.49160 NA 27.68383 126.68712 65.56192
[13] 91.86721 53.38031 80.23242 76.12746 136.49144 85.13340
[19] 103.04805 141.02757
> colSd(tmp5,na.rm=TRUE)
[1] 132.185383 9.871172 8.260379 8.348549 10.254575 11.303070
[7] 8.222726 5.957483 NA 5.261542 11.255537 8.097032
[13] 9.584738 7.306183 8.957255 8.725105 11.682955 9.226776
[19] 10.151259 11.875503
> colMax(tmp5,na.rm=TRUE)
[1] 467.41385 89.79580 85.29871 92.50879 85.35461 91.50465 78.61689
[8] 82.76007 -Inf 83.04653 91.09238 78.99579 83.27381 81.64449
[15] 94.18616 89.01180 87.67488 87.33700 84.57421 94.67726
> colMin(tmp5,na.rm=TRUE)
[1] 60.47642 58.10601 60.67143 65.15171 54.78142 59.96096 57.71813 66.26472
[9] Inf 66.41709 60.96445 56.73931 57.33560 59.14291 67.46482 65.64470
[17] 53.21259 58.90668 56.56741 54.85374
>
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 3
> which.col <- 1
> cat(which.row," ",which.col,"\n")
3 1
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> rowVars(tmp5,na.rm=TRUE)
[1] 172.2487 218.0550 273.3735 249.3815 244.3478 279.0826 279.6787 281.3080
[9] 175.6708 101.8249
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 172.2487 218.0550 273.3735 249.3815 244.3478 279.0826 279.6787 281.3080
[9] 175.6708 101.8249
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] 2.273737e-13 5.684342e-14 1.421085e-14 2.273737e-13 2.842171e-14
[6] -1.421085e-13 0.000000e+00 1.136868e-13 -8.526513e-14 8.526513e-14
[11] -1.136868e-13 2.842171e-14 2.842171e-14 1.136868e-13 2.842171e-14
[16] -1.136868e-13 2.842171e-14 8.526513e-14 -3.410605e-13 -2.842171e-14
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
8 14
5 2
5 14
5 16
1 18
3 13
3 7
2 18
7 8
10 2
7 6
7 1
3 5
4 12
1 9
2 16
10 15
3 14
2 11
10 11
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 2.699508
> Min(tmp)
[1] -1.902487
> mean(tmp)
[1] 0.02048503
> Sum(tmp)
[1] 2.048503
> Var(tmp)
[1] 0.9037545
>
> rowMeans(tmp)
[1] 0.02048503
> rowSums(tmp)
[1] 2.048503
> rowVars(tmp)
[1] 0.9037545
> rowSd(tmp)
[1] 0.95066
> rowMax(tmp)
[1] 2.699508
> rowMin(tmp)
[1] -1.902487
>
> colMeans(tmp)
[1] -0.237316516 0.756487152 -0.578853895 0.390036579 0.133304421
[6] 1.340552127 0.591475082 0.269922869 -1.175516819 0.943941458
[11] 1.048194286 1.713299892 0.443499224 -0.458454816 1.123569952
[16] 2.028443096 -1.162289910 0.932820772 -0.005761627 1.015560477
[21] -0.711401098 2.699507651 -0.608660729 0.108959992 1.161527045
[26] -0.639637387 0.257909796 0.747557766 1.331720274 0.583540711
[31] 0.450997373 1.552104153 -1.202801107 0.518985355 -1.301334868
[36] 0.104001811 -1.187320034 0.177820079 -1.669612146 0.547593846
[41] 0.187188739 -0.739616419 -0.435105580 -0.844819548 0.745564244
[46] 1.542482970 -0.009204073 -0.335161250 -1.101481985 -0.554198623
[51] 0.501400298 -0.907442990 -1.090340304 -1.104136453 -1.902486528
[56] -0.363007536 2.182495105 0.142110705 -0.336638187 0.191128874
[61] -0.320655225 1.431061371 -1.114772539 -1.081180008 -0.727087220
[66] 0.661752193 -0.468667834 -1.010102664 1.257335140 1.102219490
[71] 0.850505028 -0.598815636 -0.284376296 -0.247575385 -0.927186286
[76] -0.277511966 0.111232601 -0.041212616 0.527401887 0.953535816
[81] 0.110388273 -1.418982959 0.196826992 -0.010964375 -0.986798017
[86] -1.789934109 0.173344027 0.347497821 -0.385668609 0.222928012
[91] -1.011807674 -1.782928588 0.279679826 0.069695966 0.411384203
[96] -0.393380356 -0.982200196 -1.012993707 1.613122126 0.800291192
> colSums(tmp)
[1] -0.237316516 0.756487152 -0.578853895 0.390036579 0.133304421
[6] 1.340552127 0.591475082 0.269922869 -1.175516819 0.943941458
[11] 1.048194286 1.713299892 0.443499224 -0.458454816 1.123569952
[16] 2.028443096 -1.162289910 0.932820772 -0.005761627 1.015560477
[21] -0.711401098 2.699507651 -0.608660729 0.108959992 1.161527045
[26] -0.639637387 0.257909796 0.747557766 1.331720274 0.583540711
[31] 0.450997373 1.552104153 -1.202801107 0.518985355 -1.301334868
[36] 0.104001811 -1.187320034 0.177820079 -1.669612146 0.547593846
[41] 0.187188739 -0.739616419 -0.435105580 -0.844819548 0.745564244
[46] 1.542482970 -0.009204073 -0.335161250 -1.101481985 -0.554198623
[51] 0.501400298 -0.907442990 -1.090340304 -1.104136453 -1.902486528
[56] -0.363007536 2.182495105 0.142110705 -0.336638187 0.191128874
[61] -0.320655225 1.431061371 -1.114772539 -1.081180008 -0.727087220
[66] 0.661752193 -0.468667834 -1.010102664 1.257335140 1.102219490
[71] 0.850505028 -0.598815636 -0.284376296 -0.247575385 -0.927186286
[76] -0.277511966 0.111232601 -0.041212616 0.527401887 0.953535816
[81] 0.110388273 -1.418982959 0.196826992 -0.010964375 -0.986798017
[86] -1.789934109 0.173344027 0.347497821 -0.385668609 0.222928012
[91] -1.011807674 -1.782928588 0.279679826 0.069695966 0.411384203
[96] -0.393380356 -0.982200196 -1.012993707 1.613122126 0.800291192
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] -0.237316516 0.756487152 -0.578853895 0.390036579 0.133304421
[6] 1.340552127 0.591475082 0.269922869 -1.175516819 0.943941458
[11] 1.048194286 1.713299892 0.443499224 -0.458454816 1.123569952
[16] 2.028443096 -1.162289910 0.932820772 -0.005761627 1.015560477
[21] -0.711401098 2.699507651 -0.608660729 0.108959992 1.161527045
[26] -0.639637387 0.257909796 0.747557766 1.331720274 0.583540711
[31] 0.450997373 1.552104153 -1.202801107 0.518985355 -1.301334868
[36] 0.104001811 -1.187320034 0.177820079 -1.669612146 0.547593846
[41] 0.187188739 -0.739616419 -0.435105580 -0.844819548 0.745564244
[46] 1.542482970 -0.009204073 -0.335161250 -1.101481985 -0.554198623
[51] 0.501400298 -0.907442990 -1.090340304 -1.104136453 -1.902486528
[56] -0.363007536 2.182495105 0.142110705 -0.336638187 0.191128874
[61] -0.320655225 1.431061371 -1.114772539 -1.081180008 -0.727087220
[66] 0.661752193 -0.468667834 -1.010102664 1.257335140 1.102219490
[71] 0.850505028 -0.598815636 -0.284376296 -0.247575385 -0.927186286
[76] -0.277511966 0.111232601 -0.041212616 0.527401887 0.953535816
[81] 0.110388273 -1.418982959 0.196826992 -0.010964375 -0.986798017
[86] -1.789934109 0.173344027 0.347497821 -0.385668609 0.222928012
[91] -1.011807674 -1.782928588 0.279679826 0.069695966 0.411384203
[96] -0.393380356 -0.982200196 -1.012993707 1.613122126 0.800291192
> colMin(tmp)
[1] -0.237316516 0.756487152 -0.578853895 0.390036579 0.133304421
[6] 1.340552127 0.591475082 0.269922869 -1.175516819 0.943941458
[11] 1.048194286 1.713299892 0.443499224 -0.458454816 1.123569952
[16] 2.028443096 -1.162289910 0.932820772 -0.005761627 1.015560477
[21] -0.711401098 2.699507651 -0.608660729 0.108959992 1.161527045
[26] -0.639637387 0.257909796 0.747557766 1.331720274 0.583540711
[31] 0.450997373 1.552104153 -1.202801107 0.518985355 -1.301334868
[36] 0.104001811 -1.187320034 0.177820079 -1.669612146 0.547593846
[41] 0.187188739 -0.739616419 -0.435105580 -0.844819548 0.745564244
[46] 1.542482970 -0.009204073 -0.335161250 -1.101481985 -0.554198623
[51] 0.501400298 -0.907442990 -1.090340304 -1.104136453 -1.902486528
[56] -0.363007536 2.182495105 0.142110705 -0.336638187 0.191128874
[61] -0.320655225 1.431061371 -1.114772539 -1.081180008 -0.727087220
[66] 0.661752193 -0.468667834 -1.010102664 1.257335140 1.102219490
[71] 0.850505028 -0.598815636 -0.284376296 -0.247575385 -0.927186286
[76] -0.277511966 0.111232601 -0.041212616 0.527401887 0.953535816
[81] 0.110388273 -1.418982959 0.196826992 -0.010964375 -0.986798017
[86] -1.789934109 0.173344027 0.347497821 -0.385668609 0.222928012
[91] -1.011807674 -1.782928588 0.279679826 0.069695966 0.411384203
[96] -0.393380356 -0.982200196 -1.012993707 1.613122126 0.800291192
> colMedians(tmp)
[1] -0.237316516 0.756487152 -0.578853895 0.390036579 0.133304421
[6] 1.340552127 0.591475082 0.269922869 -1.175516819 0.943941458
[11] 1.048194286 1.713299892 0.443499224 -0.458454816 1.123569952
[16] 2.028443096 -1.162289910 0.932820772 -0.005761627 1.015560477
[21] -0.711401098 2.699507651 -0.608660729 0.108959992 1.161527045
[26] -0.639637387 0.257909796 0.747557766 1.331720274 0.583540711
[31] 0.450997373 1.552104153 -1.202801107 0.518985355 -1.301334868
[36] 0.104001811 -1.187320034 0.177820079 -1.669612146 0.547593846
[41] 0.187188739 -0.739616419 -0.435105580 -0.844819548 0.745564244
[46] 1.542482970 -0.009204073 -0.335161250 -1.101481985 -0.554198623
[51] 0.501400298 -0.907442990 -1.090340304 -1.104136453 -1.902486528
[56] -0.363007536 2.182495105 0.142110705 -0.336638187 0.191128874
[61] -0.320655225 1.431061371 -1.114772539 -1.081180008 -0.727087220
[66] 0.661752193 -0.468667834 -1.010102664 1.257335140 1.102219490
[71] 0.850505028 -0.598815636 -0.284376296 -0.247575385 -0.927186286
[76] -0.277511966 0.111232601 -0.041212616 0.527401887 0.953535816
[81] 0.110388273 -1.418982959 0.196826992 -0.010964375 -0.986798017
[86] -1.789934109 0.173344027 0.347497821 -0.385668609 0.222928012
[91] -1.011807674 -1.782928588 0.279679826 0.069695966 0.411384203
[96] -0.393380356 -0.982200196 -1.012993707 1.613122126 0.800291192
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.2373165 0.7564872 -0.5788539 0.3900366 0.1333044 1.340552 0.5914751
[2,] -0.2373165 0.7564872 -0.5788539 0.3900366 0.1333044 1.340552 0.5914751
[,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15]
[1,] 0.2699229 -1.175517 0.9439415 1.048194 1.7133 0.4434992 -0.4584548 1.12357
[2,] 0.2699229 -1.175517 0.9439415 1.048194 1.7133 0.4434992 -0.4584548 1.12357
[,16] [,17] [,18] [,19] [,20] [,21] [,22]
[1,] 2.028443 -1.16229 0.9328208 -0.005761627 1.01556 -0.7114011 2.699508
[2,] 2.028443 -1.16229 0.9328208 -0.005761627 1.01556 -0.7114011 2.699508
[,23] [,24] [,25] [,26] [,27] [,28] [,29]
[1,] -0.6086607 0.10896 1.161527 -0.6396374 0.2579098 0.7475578 1.33172
[2,] -0.6086607 0.10896 1.161527 -0.6396374 0.2579098 0.7475578 1.33172
[,30] [,31] [,32] [,33] [,34] [,35] [,36]
[1,] 0.5835407 0.4509974 1.552104 -1.202801 0.5189854 -1.301335 0.1040018
[2,] 0.5835407 0.4509974 1.552104 -1.202801 0.5189854 -1.301335 0.1040018
[,37] [,38] [,39] [,40] [,41] [,42] [,43]
[1,] -1.18732 0.1778201 -1.669612 0.5475938 0.1871887 -0.7396164 -0.4351056
[2,] -1.18732 0.1778201 -1.669612 0.5475938 0.1871887 -0.7396164 -0.4351056
[,44] [,45] [,46] [,47] [,48] [,49] [,50]
[1,] -0.8448195 0.7455642 1.542483 -0.009204073 -0.3351612 -1.101482 -0.5541986
[2,] -0.8448195 0.7455642 1.542483 -0.009204073 -0.3351612 -1.101482 -0.5541986
[,51] [,52] [,53] [,54] [,55] [,56] [,57]
[1,] 0.5014003 -0.907443 -1.09034 -1.104136 -1.902487 -0.3630075 2.182495
[2,] 0.5014003 -0.907443 -1.09034 -1.104136 -1.902487 -0.3630075 2.182495
[,58] [,59] [,60] [,61] [,62] [,63] [,64]
[1,] 0.1421107 -0.3366382 0.1911289 -0.3206552 1.431061 -1.114773 -1.08118
[2,] 0.1421107 -0.3366382 0.1911289 -0.3206552 1.431061 -1.114773 -1.08118
[,65] [,66] [,67] [,68] [,69] [,70] [,71]
[1,] -0.7270872 0.6617522 -0.4686678 -1.010103 1.257335 1.102219 0.850505
[2,] -0.7270872 0.6617522 -0.4686678 -1.010103 1.257335 1.102219 0.850505
[,72] [,73] [,74] [,75] [,76] [,77]
[1,] -0.5988156 -0.2843763 -0.2475754 -0.9271863 -0.277512 0.1112326
[2,] -0.5988156 -0.2843763 -0.2475754 -0.9271863 -0.277512 0.1112326
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -0.04121262 0.5274019 0.9535358 0.1103883 -1.418983 0.196827 -0.01096438
[2,] -0.04121262 0.5274019 0.9535358 0.1103883 -1.418983 0.196827 -0.01096438
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -0.986798 -1.789934 0.173344 0.3474978 -0.3856686 0.222928 -1.011808
[2,] -0.986798 -1.789934 0.173344 0.3474978 -0.3856686 0.222928 -1.011808
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -1.782929 0.2796798 0.06969597 0.4113842 -0.3933804 -0.9822002 -1.012994
[2,] -1.782929 0.2796798 0.06969597 0.4113842 -0.3933804 -0.9822002 -1.012994
[,99] [,100]
[1,] 1.613122 0.8002912
[2,] 1.613122 0.8002912
>
>
> Max(tmp2)
[1] 2.276056
> Min(tmp2)
[1] -3.612607
> mean(tmp2)
[1] -0.1429673
> Sum(tmp2)
[1] -14.29673
> Var(tmp2)
[1] 1.248658
>
> rowMeans(tmp2)
[1] -0.15649640 -1.19076517 2.17392520 -1.01958142 0.57118454 -0.12336702
[7] 0.74437363 -0.23810371 -0.35249386 -0.28250934 1.26303220 -0.18697037
[13] -1.05317354 0.98962913 -1.92018227 -2.63408670 0.30253757 1.03469626
[19] -1.79189548 -1.59408498 0.50048853 2.19452909 0.31454015 0.12538015
[25] 1.20375627 -0.80255784 -0.91210302 0.05935709 -2.30387763 -0.05824447
[31] -0.55081057 -0.18210292 1.71598698 -1.64390346 -1.54544570 0.10050673
[37] -0.92983942 -0.77147560 -0.52780909 -2.35155527 1.86598371 0.41833003
[43] 0.01315788 2.27605615 0.84383366 0.14482328 -1.17935531 0.31077585
[49] 0.75367246 -1.93592651 -0.57541450 0.12051856 0.51745263 -0.32622346
[55] 1.52031094 -0.99365061 -0.74427134 1.08347323 -1.06395722 -0.77804397
[61] -1.63644957 0.82843760 -0.47211063 -0.49345912 -0.90159602 1.35900283
[67] -0.86361546 -0.55622885 2.19302517 1.01725768 0.12619349 -0.64773598
[73] -0.67506254 -0.36570240 -0.49389416 -0.13118133 0.83080802 -0.99087826
[79] -0.78542909 -0.99759682 -0.19358225 0.17917680 -0.23351231 0.18968751
[85] 0.59283355 -0.44105679 2.20364680 0.10401851 1.01875054 -0.11184593
[91] 1.11371409 -3.61260657 -0.87349222 -0.11117134 -0.08084815 0.66171286
[97] -0.62306145 0.61243651 0.30074770 -1.77809326
> rowSums(tmp2)
[1] -0.15649640 -1.19076517 2.17392520 -1.01958142 0.57118454 -0.12336702
[7] 0.74437363 -0.23810371 -0.35249386 -0.28250934 1.26303220 -0.18697037
[13] -1.05317354 0.98962913 -1.92018227 -2.63408670 0.30253757 1.03469626
[19] -1.79189548 -1.59408498 0.50048853 2.19452909 0.31454015 0.12538015
[25] 1.20375627 -0.80255784 -0.91210302 0.05935709 -2.30387763 -0.05824447
[31] -0.55081057 -0.18210292 1.71598698 -1.64390346 -1.54544570 0.10050673
[37] -0.92983942 -0.77147560 -0.52780909 -2.35155527 1.86598371 0.41833003
[43] 0.01315788 2.27605615 0.84383366 0.14482328 -1.17935531 0.31077585
[49] 0.75367246 -1.93592651 -0.57541450 0.12051856 0.51745263 -0.32622346
[55] 1.52031094 -0.99365061 -0.74427134 1.08347323 -1.06395722 -0.77804397
[61] -1.63644957 0.82843760 -0.47211063 -0.49345912 -0.90159602 1.35900283
[67] -0.86361546 -0.55622885 2.19302517 1.01725768 0.12619349 -0.64773598
[73] -0.67506254 -0.36570240 -0.49389416 -0.13118133 0.83080802 -0.99087826
[79] -0.78542909 -0.99759682 -0.19358225 0.17917680 -0.23351231 0.18968751
[85] 0.59283355 -0.44105679 2.20364680 0.10401851 1.01875054 -0.11184593
[91] 1.11371409 -3.61260657 -0.87349222 -0.11117134 -0.08084815 0.66171286
[97] -0.62306145 0.61243651 0.30074770 -1.77809326
> rowVars(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowSd(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowMax(tmp2)
[1] -0.15649640 -1.19076517 2.17392520 -1.01958142 0.57118454 -0.12336702
[7] 0.74437363 -0.23810371 -0.35249386 -0.28250934 1.26303220 -0.18697037
[13] -1.05317354 0.98962913 -1.92018227 -2.63408670 0.30253757 1.03469626
[19] -1.79189548 -1.59408498 0.50048853 2.19452909 0.31454015 0.12538015
[25] 1.20375627 -0.80255784 -0.91210302 0.05935709 -2.30387763 -0.05824447
[31] -0.55081057 -0.18210292 1.71598698 -1.64390346 -1.54544570 0.10050673
[37] -0.92983942 -0.77147560 -0.52780909 -2.35155527 1.86598371 0.41833003
[43] 0.01315788 2.27605615 0.84383366 0.14482328 -1.17935531 0.31077585
[49] 0.75367246 -1.93592651 -0.57541450 0.12051856 0.51745263 -0.32622346
[55] 1.52031094 -0.99365061 -0.74427134 1.08347323 -1.06395722 -0.77804397
[61] -1.63644957 0.82843760 -0.47211063 -0.49345912 -0.90159602 1.35900283
[67] -0.86361546 -0.55622885 2.19302517 1.01725768 0.12619349 -0.64773598
[73] -0.67506254 -0.36570240 -0.49389416 -0.13118133 0.83080802 -0.99087826
[79] -0.78542909 -0.99759682 -0.19358225 0.17917680 -0.23351231 0.18968751
[85] 0.59283355 -0.44105679 2.20364680 0.10401851 1.01875054 -0.11184593
[91] 1.11371409 -3.61260657 -0.87349222 -0.11117134 -0.08084815 0.66171286
[97] -0.62306145 0.61243651 0.30074770 -1.77809326
> rowMin(tmp2)
[1] -0.15649640 -1.19076517 2.17392520 -1.01958142 0.57118454 -0.12336702
[7] 0.74437363 -0.23810371 -0.35249386 -0.28250934 1.26303220 -0.18697037
[13] -1.05317354 0.98962913 -1.92018227 -2.63408670 0.30253757 1.03469626
[19] -1.79189548 -1.59408498 0.50048853 2.19452909 0.31454015 0.12538015
[25] 1.20375627 -0.80255784 -0.91210302 0.05935709 -2.30387763 -0.05824447
[31] -0.55081057 -0.18210292 1.71598698 -1.64390346 -1.54544570 0.10050673
[37] -0.92983942 -0.77147560 -0.52780909 -2.35155527 1.86598371 0.41833003
[43] 0.01315788 2.27605615 0.84383366 0.14482328 -1.17935531 0.31077585
[49] 0.75367246 -1.93592651 -0.57541450 0.12051856 0.51745263 -0.32622346
[55] 1.52031094 -0.99365061 -0.74427134 1.08347323 -1.06395722 -0.77804397
[61] -1.63644957 0.82843760 -0.47211063 -0.49345912 -0.90159602 1.35900283
[67] -0.86361546 -0.55622885 2.19302517 1.01725768 0.12619349 -0.64773598
[73] -0.67506254 -0.36570240 -0.49389416 -0.13118133 0.83080802 -0.99087826
[79] -0.78542909 -0.99759682 -0.19358225 0.17917680 -0.23351231 0.18968751
[85] 0.59283355 -0.44105679 2.20364680 0.10401851 1.01875054 -0.11184593
[91] 1.11371409 -3.61260657 -0.87349222 -0.11117134 -0.08084815 0.66171286
[97] -0.62306145 0.61243651 0.30074770 -1.77809326
>
> colMeans(tmp2)
[1] -0.1429673
> colSums(tmp2)
[1] -14.29673
> colVars(tmp2)
[1] 1.248658
> colSd(tmp2)
[1] 1.117434
> colMax(tmp2)
[1] 2.276056
> colMin(tmp2)
[1] -3.612607
> colMedians(tmp2)
[1] -0.1692997
> colRanges(tmp2)
[,1]
[1,] -3.612607
[2,] 2.276056
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] 1.8552854 0.2324811 -1.0976222 -1.0921930 0.1069016 3.4303478
[7] 2.3245960 2.9160768 6.8206568 0.6652462
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.10955620
[2,] -0.02116798
[3,] 0.31707686
[4,] 0.48562763
[5,] 0.97712233
>
> rowApply(tmp,sum)
[1] 3.6943655 -0.4910858 2.1167447 2.7563274 4.5329809 1.0835855
[7] -0.7658835 1.7052609 1.7708779 -0.2413971
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 7 7 2 3 6 9 6 8 5 4
[2,] 3 2 3 5 8 8 4 9 1 9
[3,] 10 6 4 1 5 5 2 6 10 1
[4,] 2 4 7 7 4 1 1 4 3 6
[5,] 1 10 8 10 1 7 3 3 2 2
[6,] 8 8 6 8 2 10 7 1 4 8
[7,] 5 1 9 6 3 3 5 7 6 10
[8,] 4 5 5 2 10 2 9 10 8 7
[9,] 9 9 10 4 9 4 8 2 9 5
[10,] 6 3 1 9 7 6 10 5 7 3
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 1.60794674 -0.55404787 -2.75945052 -2.75823058 0.03925612 -1.20375399
[7] -1.76308047 -1.34308928 2.97282290 0.43169740 -2.79918811 0.51168853
[13] -0.10242410 -0.12672667 0.49543479 0.54466680 -0.48831176 0.23392504
[19] 0.58126515 -1.22913225
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.71740745
[2,] 0.04851476
[3,] 0.36600433
[4,] 0.64925876
[5,] 1.26157634
>
> rowApply(tmp,sum)
[1] -4.5850891 8.8441517 -9.1718147 -0.6518019 -2.1441782
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 8 17 17 10 13
[2,] 10 13 3 19 6
[3,] 9 1 1 14 19
[4,] 1 12 15 6 3
[5,] 4 20 11 9 5
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.71740745 -0.3470173 -0.5527498 -1.9414674 -1.0470910 0.7142023
[2,] 1.26157634 0.7585896 -1.2441639 0.6503488 2.6092526 1.2884631
[3,] 0.64925876 -1.4595830 -2.5467833 0.4313625 -0.5382360 -0.8031151
[4,] 0.04851476 1.1722705 0.5489018 -0.7350623 -0.1423530 -1.5152595
[5,] 0.36600433 -0.6783078 1.0353447 -1.1634122 -0.8423164 -0.8880448
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.03865109 -1.7059695 2.0115037 -1.0442342 -0.1656698 0.6476455
[2,] -1.04661820 0.2947683 0.4619631 0.7924858 -0.6448782 0.5665662
[3,] -1.36137914 -1.2063600 0.5306603 0.3681416 -2.1942252 -0.5543630
[4,] 0.65920349 0.8668206 -0.6513368 0.8214941 -0.9240284 0.1264441
[5,] -0.05293771 0.4076513 0.6200327 -0.5061899 1.1296134 -0.2746043
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.02997449 0.03193654 0.04596638 -1.06453188 -1.013231780 1.5391713
[2,] -0.69157200 0.83006497 -0.03199515 -0.05119974 0.005947193 1.7301013
[3,] 1.53821950 1.34485447 -1.23587287 0.75104612 -1.222083027 -0.2868247
[4,] -0.65640043 -1.08616621 2.07751777 0.15096505 1.010912959 -1.0700339
[5,] -0.26269669 -1.24741643 -0.36018134 0.75838725 0.730142898 -1.6784889
[,19] [,20]
[1,] -0.721655937 0.7368346
[2,] 0.782487741 0.5219639
[3,] -0.004018672 -1.3725139
[4,] 0.522880126 -1.8770865
[5,] 0.001571893 0.7616697
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.8 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 631 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 543 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.8 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 1.335633 0.283695 1.025389 0.4627117 0.8155893 -1.262374 0.6588332
col8 col9 col10 col11 col12 col13 col14
row1 1.394031 -3.038603 -0.4964582 -1.882741 -0.8581568 0.5608016 -0.3389617
col15 col16 col17 col18 col19 col20
row1 0.8771792 -0.8427552 0.2443815 1.485544 0.4818963 -0.60207
> tmp[,"col10"]
col10
row1 -0.4964582
row2 -1.4605421
row3 0.1850158
row4 0.9718559
row5 -1.0920336
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 1.3356326 0.2836950 1.0253886 0.4627117 0.8155893 -1.2623736 0.6588332
row5 -0.3467699 -0.8267825 0.2721228 0.5220366 0.5233992 0.2266246 -1.1852765
col8 col9 col10 col11 col12 col13 col14
row1 1.3940311 -3.038603 -0.4964582 -1.882741 -0.8581568 0.5608016 -0.3389617
row5 0.6056213 -1.214606 -1.0920336 1.549636 -0.6431711 -1.2337191 1.2600049
col15 col16 col17 col18 col19 col20
row1 0.8771792 -0.8427552 0.2443815 1.485544 0.4818963 -0.602070
row5 0.7967598 -0.8975552 1.1681380 1.697015 1.3693694 -2.158605
> tmp[,c("col6","col20")]
col6 col20
row1 -1.2623736 -0.6020700
row2 0.5634085 1.0776832
row3 -0.4745183 -0.1257047
row4 -0.8469694 0.4774756
row5 0.2266246 -2.1586055
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -1.2623736 -0.602070
row5 0.2266246 -2.158605
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 52.07871 50.2422 49.92772 49.35689 51.1301 105.5945 49.86616 50.99773
col9 col10 col11 col12 col13 col14 col15 col16
row1 48.0198 50.5845 50.82146 50.53653 50.06404 51.12146 51.1198 48.59282
col17 col18 col19 col20
row1 50.19995 50.21292 50.83061 102.8604
> tmp[,"col10"]
col10
row1 50.58450
row2 30.11520
row3 30.33980
row4 27.21958
row5 49.97528
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 52.07871 50.24220 49.92772 49.35689 51.13010 105.5945 49.86616 50.99773
row5 50.59841 51.25451 51.44063 49.00823 50.17702 104.9897 50.27749 48.61102
col9 col10 col11 col12 col13 col14 col15 col16
row1 48.01980 50.58450 50.82146 50.53653 50.06404 51.12146 51.11980 48.59282
row5 50.84853 49.97528 51.37990 51.22229 50.75663 51.22587 50.13072 49.98986
col17 col18 col19 col20
row1 50.19995 50.21292 50.83061 102.8604
row5 48.77629 50.41379 49.57923 104.8029
> tmp[,c("col6","col20")]
col6 col20
row1 105.59446 102.86039
row2 75.92651 74.93285
row3 74.16575 75.12283
row4 74.93828 74.52246
row5 104.98969 104.80291
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.5945 102.8604
row5 104.9897 104.8029
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.5945 102.8604
row5 104.9897 104.8029
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.24371177
[2,] -0.79327940
[3,] -1.31179300
[4,] -1.53856187
[5,] -0.01259777
> tmp[,c("col17","col7")]
col17 col7
[1,] 1.14518328 -2.53964476
[2,] -0.93041032 0.33415800
[3,] 0.99987802 -1.32591131
[4,] 1.22129792 0.11165806
[5,] -0.06300081 -0.04995291
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.04663984 -0.7195815
[2,] -0.58432565 0.4154939
[3,] 0.01924370 -0.6583731
[4,] -1.00691817 -1.1892459
[5,] -1.02113104 0.3324005
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.04663984
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.04663984
[2,] -0.58432565
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6]
row3 1.4520914 -2.2948860 -0.01092824 0.09836194 0.6365028 -0.7390750
row1 -0.9082684 0.6091533 1.03419654 0.50673461 -0.2823089 -0.4189507
[,7] [,8] [,9] [,10] [,11] [,12]
row3 1.163326 -0.29253241 -0.7719049 0.4432124 1.2815023 -0.1312828
row1 -1.302848 0.02537992 -0.1155067 -2.4677074 0.6135201 -0.2798424
[,13] [,14] [,15] [,16] [,17] [,18]
row3 -0.8959776 0.5405798 0.6397908 -0.4680180 0.5718591 -0.639111049
row1 -1.0616927 -0.5589013 -0.7034370 0.8589092 -0.9533357 0.008986276
[,19] [,20]
row3 -0.9545212 -1.3290183
row1 -0.7511114 0.2618587
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -0.7565766 -1.114743 0.8303536 -0.1204095 0.2639552 -0.5681038 -1.46633
[,8] [,9] [,10]
row2 -0.4771076 -0.1581652 -0.07674378
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -0.1118608 -1.153622 0.541419 -0.3503934 0.4271899 0.2316941 0.6330384
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.8646508 -0.4559199 0.7136559 1.656988 0.3030107 -0.2098769 -0.2503136
[,15] [,16] [,17] [,18] [,19] [,20]
row5 1.426114 1.297437 -0.8844593 1.962301 1.367027 -0.2004142
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> colnames(tmp) <- NULL
> rownames(tmp) <- NULL
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
> dimnames(tmp) <- NULL
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
> dimnames(tmp) <- NULL
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
NULL
>
> dimnames(tmp) <- list(NULL,c(colnames(tmp,do.NULL=FALSE)))
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
>
> ###
> ### Testing logical indexing
> ###
> ###
>
> tmp <- createBufferedMatrix(230,15)
> tmp[1:230,1:15] <- rnorm(230*15)
> x <-tmp[1:230,1:15]
>
> for (rep in 1:10){
+ which.cols <- sample(c(TRUE,FALSE),15,replace=T)
+ which.rows <- sample(c(TRUE,FALSE),230,replace=T)
+
+ if (!all(tmp[which.rows,which.cols] == x[which.rows,which.cols])){
+ stop("No agreement when logical indexing\n")
+ }
+
+ if (!all(subBufferedMatrix(tmp,,which.cols)[,1:sum(which.cols)] == x[,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix cols\n")
+ }
+ if (!all(subBufferedMatrix(tmp,which.rows,)[1:sum(which.rows),] == x[which.rows,])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows\n")
+ }
+
+
+ if (!all(subBufferedMatrix(tmp,which.rows,which.cols)[1:sum(which.rows),1:sum(which.cols)]== x[which.rows,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows and columns\n")
+ }
+ }
>
>
> ##
> ## Test the ReadOnlyMode
> ##
>
> ReadOnlyMode(tmp)
<pointer: 0x000001a7606ff770>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM20d5c1bfc1463"
[2] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM20d5c5975271c"
[3] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM20d5c307f227f"
[4] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM20d5c32755f66"
[5] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM20d5c56067dfe"
[6] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM20d5c160343d9"
[7] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM20d5c27947e0"
[8] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM20d5caf0295"
[9] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM20d5c13164d76"
[10] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM20d5c241a728f"
[11] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM20d5c24fe3576"
[12] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM20d5c49334942"
[13] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM20d5c372f34b"
[14] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM20d5c7cc458a2"
[15] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM20d5c71924ae"
>
>
> ### testing coercion functions
> ###
>
> tmp <- as(tmp,"matrix")
> tmp <- as(tmp,"BufferedMatrix")
>
>
>
> ### testing whether can move storage from one location to another
>
> MoveStorageDirectory(tmp,"NewDirectory",full.path=FALSE)
<pointer: 0x000001a7632ff110>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x000001a7632ff110>
Warning message:
In dir.create(new.directory) :
'F:\biocbuild\bbs-3.20-bioc\meat\BufferedMatrix.Rcheck\tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x000001a7632ff110>
> rowMedians(tmp)
[1] -0.383496839 0.364187005 0.019638573 -0.044776192 -0.134013293
[6] -0.111402414 -0.031317453 0.426093315 0.087340510 -0.277701012
[11] 0.132401104 0.307976310 -0.013954078 0.808055313 0.118589313
[16] 0.061658989 -0.395636078 -0.048287151 0.066100118 0.235762642
[21] 0.064554007 -0.343079728 0.254666284 0.446555940 0.392374607
[26] -0.209912830 0.515047426 0.478026980 -0.438747926 -0.218582657
[31] -0.202897479 -0.002071485 -0.211806823 0.296783308 -0.089750039
[36] -0.273954283 0.287690918 -0.434879427 -0.196032109 0.079660475
[41] 0.345839544 0.100597573 -0.572908288 0.120033308 -0.230733590
[46] -0.162143105 0.458228400 0.096459233 0.195822387 0.187016062
[51] 0.618344327 0.227969572 0.349506085 0.077792527 0.096676728
[56] -0.162465230 0.318223060 0.359825271 0.448577969 0.173749764
[61] -0.539767193 -0.833608977 0.109774974 -0.147800596 0.200925627
[66] 0.409965870 -0.480515946 0.388062163 -0.341356856 0.109875478
[71] -0.583730542 0.110576038 -0.250014984 -0.233176361 -0.286576507
[76] -0.289482465 -0.155281152 0.124182423 -0.357240336 0.253740360
[81] -0.423345058 0.103482426 -0.243992982 -0.459067311 0.009843509
[86] -0.374741630 -0.730534298 0.063942360 -0.285742100 -0.176628484
[91] 0.241300371 -0.411045293 0.311572094 0.466477901 0.343521043
[96] -0.065110553 -0.071812761 -0.336811497 0.016657701 -0.115907064
[101] -0.495036590 -0.210088211 0.009889550 -0.367442001 -0.153158069
[106] -0.055608764 0.165695556 -0.355842524 -0.331493140 -0.112190919
[111] 0.423003212 -0.583722052 0.094688362 0.070555103 0.136838418
[116] 0.015966094 -0.127837831 -0.162500930 -0.724085918 -0.110871634
[121] 0.542066795 -0.418103273 -0.340915169 0.007355288 0.244055942
[126] 0.249786576 0.044606818 -0.123068555 -0.297460237 -0.659900881
[131] -0.077153984 -0.391022374 0.299940740 -0.608656889 -0.273985728
[136] -0.060020280 -0.134067564 0.089917054 -0.110753169 0.091869131
[141] -0.173591881 0.155847866 0.310961897 -0.613072746 0.158016071
[146] 0.253995491 0.140206089 -0.533070001 -0.109898921 -0.186191966
[151] -0.001931790 0.511651315 -0.002742843 0.016097896 0.024587639
[156] 0.197451683 -0.339630049 -0.132855492 0.055176436 0.370407936
[161] 0.200454697 -0.021972742 0.263815613 0.480057640 -0.060306242
[166] 0.073739041 -0.025894697 0.118170347 -0.546762670 0.463889997
[171] 0.078690626 -0.794595390 -0.633313106 0.043207560 0.333595165
[176] 0.140653959 -0.237843469 0.072236077 -0.038131898 -0.363076698
[181] 0.044586373 -0.088495145 -0.375223408 0.310512883 -0.023466559
[186] 0.092793204 0.333029839 0.248526436 -0.317466993 0.428686421
[191] -0.074880144 -0.052583494 -0.128971321 -0.107971571 0.351460335
[196] -0.209650399 -0.544857253 0.248278312 -0.007795779 0.328861848
[201] -0.168527757 0.037912174 -0.059609382 -0.781588189 0.237127254
[206] 0.202217193 0.451159126 -0.112893193 -0.032063142 0.162685898
[211] -0.576788543 -0.645835793 0.345005858 0.174518556 -0.126172340
[216] 0.550187627 -0.328485595 0.050657355 -0.146041804 -0.134924970
[221] -0.061331623 -0.036317003 0.265610592 0.100013123 -0.535083077
[226] -0.101242942 -0.011301384 -0.092204759 -0.207551306 -0.045105883
>
> proc.time()
user system elapsed
3.70 20.07 119.03
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> prefix <- "dbmtest"
> directory <- getwd()
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x00000253dc0ffb30>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x00000253dc0ffb30>
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x00000253dc0ffb30>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000 0.000000 0.000000 0.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000 0.000000 0.000000 0.000000 0.000000
<pointer: 0x00000253dc0ffb30>
> rm(P)
>
> #P <- .Call("R_bm_Destroy",P)
> #.Call("R_bm_Destroy",P)
> #.Call("R_bm_Test_C",P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 0
Buffer Rows: 1
Buffer Cols: 1
Printing Values
<pointer: 0x00000253dc0ff470>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000253dc0ff470>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 1
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000
0.000000
0.000000
0.000000
0.000000
<pointer: 0x00000253dc0ff470>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000253dc0ff470>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x00000253dc0ff470>
> rm(P)
>
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000253dc0ff6b0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000253dc0ff6b0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x00000253dc0ff6b0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x00000253dc0ff6b0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x00000253dc0ff6b0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x00000253dc0ff6b0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x00000253dc0ff6b0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x00000253dc0ff6b0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x00000253dc0ff6b0>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000253dc0ffdd0>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x00000253dc0ffdd0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000253dc0ffdd0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000253dc0ffdd0>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1263c5ca356eb" "BufferedMatrixFile1263c6759142e"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1263c5ca356eb" "BufferedMatrixFile1263c6759142e"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000253dc5676b0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000253dc5676b0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x00000253dc5676b0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x00000253dc5676b0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x00000253dc5676b0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x00000253dc5676b0>
> .Call("R_bm_isRowMode",P)
[1] FALSE
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000253dc567410>
> .Call("R_bm_AddColumn",P)
<pointer: 0x00000253dc567410>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x00000253dc567410>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x00000253dc567410>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x00000253dc5677d0>
> .Call("R_bm_getValue",P,3,3)
[1] 6
>
> .Call("R_bm_getValue",P,100000,10000)
[1] NA
> .Call("R_bm_setValue",P,3,3,12345.0)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 12345.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x00000253dc5677d0>
> rm(P)
>
> proc.time()
user system elapsed
0.25 0.14 0.57
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.32 0.09 0.37