Ben Bolstad
| Snapshot Date: 2024-05-30 18:57:37 -0400 (Thu, 30 May 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 2024-05-31 19:28:42 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
| 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 244/2233 | 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 | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BufferedMatrix_1.69.0.tar.gz |
| StartedAt: 2024-05-31 02:03:12 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 02:03:35 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 23.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BufferedMatrix_1.69.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BufferedMatrix’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 loading without being on the library search path ... 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 is not available
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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){
| ^~~~~~~~~~~~~~~~~~~
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"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init_package.c -o init_package.o
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** 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 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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
0.259 0.034 0.284
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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] "/home/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 471778 25.2 1026220 54.9 643434 34.4
Vcells 871903 6.7 8388608 64.0 2046581 15.7
>
>
>
>
> ##
> ## 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] "Fri May 31 02:03:27 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] "Fri May 31 02:03:28 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: 0x56274865b6b0>
>
>
>
> 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] "Fri May 31 02:03:28 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] "Fri May 31 02:03:28 2024"
>
> ColMode(tmp2)
<pointer: 0x56274865b6b0>
>
>
>
> ### 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,] 101.6769446 -0.8217051 0.2422547 0.05530443
[2,] -0.5858630 -0.1143296 1.2781584 0.32590845
[3,] 1.7278494 -0.7850418 -0.6795149 0.31686469
[4,] -0.6751125 0.6866792 -1.5896633 -0.92913842
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 101.6769446 0.8217051 0.2422547 0.05530443
[2,] 0.5858630 0.1143296 1.2781584 0.32590845
[3,] 1.7278494 0.7850418 0.6795149 0.31686469
[4,] 0.6751125 0.6866792 1.5896633 0.92913842
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 10.0834986 0.9064795 0.4921938 0.2351689
[2,] 0.7654169 0.3381266 1.1305567 0.5708839
[3,] 1.3144769 0.8860258 0.8243269 0.5629074
[4,] 0.8216523 0.8286611 1.2608185 0.9639183
>
> 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: /home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 227.51193 34.88650 30.16419 27.40699
[2,] 33.24003 28.49560 37.58373 31.03475
[3,] 39.87262 34.64530 33.92278 30.94594
[4,] 33.89164 33.97329 39.19785 35.56832
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x56274750c530>
> exp(tmp5)
<pointer: 0x56274750c530>
> log(tmp5,2)
<pointer: 0x56274750c530>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 473.5363
> Min(tmp5)
[1] 54.3891
> mean(tmp5)
[1] 71.45336
> Sum(tmp5)
[1] 14290.67
> Var(tmp5)
[1] 878.4627
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 89.73725 70.11865 69.38054 67.87043 69.68651 69.10518 71.06093 69.94240
[9] 68.08015 69.55160
> rowSums(tmp5)
[1] 1794.745 1402.373 1387.611 1357.409 1393.730 1382.104 1421.219 1398.848
[9] 1361.603 1391.032
> rowVars(tmp5)
[1] 8217.24169 44.40166 40.76554 70.58772 107.21898 54.77081
[7] 61.33131 35.41393 84.88415 84.87870
> rowSd(tmp5)
[1] 90.649003 6.663457 6.384790 8.401650 10.354660 7.400730 7.831431
[8] 5.950960 9.213260 9.212964
> rowMax(tmp5)
[1] 473.53628 80.29548 82.98963 92.64781 89.33946 90.47666 85.87125
[8] 79.31017 91.43643 88.16632
> rowMin(tmp5)
[1] 57.04407 59.30985 57.49901 54.38910 54.46750 56.87122 55.80980 57.19926
[9] 54.47547 55.96660
>
> colMeans(tmp5)
[1] 108.17714 71.98048 69.24573 70.24941 67.95051 70.11946 67.31418
[8] 66.45897 69.87140 69.50380 69.68957 70.84890 71.38298 65.97849
[15] 70.60462 67.79053 69.95409 72.62351 69.32358 69.99993
> colSums(tmp5)
[1] 1081.7714 719.8048 692.4573 702.4941 679.5051 701.1946 673.1418
[8] 664.5897 698.7140 695.0380 696.8957 708.4890 713.8298 659.7849
[15] 706.0462 677.9053 699.5409 726.2351 693.2358 699.9993
> colVars(tmp5)
[1] 16533.27377 69.38894 104.01376 74.30957 34.89506 53.42207
[7] 15.16006 63.78695 33.21972 120.36759 18.26978 72.87095
[13] 133.01796 49.57443 66.61316 43.39931 78.83912 64.04114
[19] 49.86647 105.98486
> colSd(tmp5)
[1] 128.581779 8.330002 10.198714 8.620300 5.907204 7.309040
[7] 3.893592 7.986673 5.763655 10.971216 4.274316 8.536448
[13] 11.533341 7.040911 8.161688 6.587815 8.879140 8.002571
[19] 7.061620 10.294895
> colMax(tmp5)
[1] 473.53628 85.80689 83.86949 88.16632 77.78591 80.38661 76.66692
[8] 79.64810 82.40429 87.36468 76.19193 90.47666 92.64781 77.94739
[15] 82.07841 77.80338 85.87125 86.54254 79.31017 91.43643
> colMin(tmp5)
[1] 57.79595 58.57917 54.47547 57.04407 56.16488 55.80980 62.02136 54.38910
[9] 64.77587 56.87122 63.31363 57.73316 57.98204 54.46750 55.96660 59.43149
[17] 59.36992 59.67869 60.51280 57.17098
>
>
> ### 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] 89.73725 70.11865 NA 67.87043 69.68651 69.10518 71.06093 69.94240
[9] 68.08015 69.55160
> rowSums(tmp5)
[1] 1794.745 1402.373 NA 1357.409 1393.730 1382.104 1421.219 1398.848
[9] 1361.603 1391.032
> rowVars(tmp5)
[1] 8217.24169 44.40166 34.77470 70.58772 107.21898 54.77081
[7] 61.33131 35.41393 84.88415 84.87870
> rowSd(tmp5)
[1] 90.649003 6.663457 5.897008 8.401650 10.354660 7.400730 7.831431
[8] 5.950960 9.213260 9.212964
> rowMax(tmp5)
[1] 473.53628 80.29548 NA 92.64781 89.33946 90.47666 85.87125
[8] 79.31017 91.43643 88.16632
> rowMin(tmp5)
[1] 57.04407 59.30985 NA 54.38910 54.46750 56.87122 55.80980 57.19926
[9] 54.47547 55.96660
>
> colMeans(tmp5)
[1] 108.17714 71.98048 69.24573 70.24941 67.95051 70.11946 67.31418
[8] 66.45897 69.87140 NA 69.68957 70.84890 71.38298 65.97849
[15] 70.60462 67.79053 69.95409 72.62351 69.32358 69.99993
> colSums(tmp5)
[1] 1081.7714 719.8048 692.4573 702.4941 679.5051 701.1946 673.1418
[8] 664.5897 698.7140 NA 696.8957 708.4890 713.8298 659.7849
[15] 706.0462 677.9053 699.5409 726.2351 693.2358 699.9993
> colVars(tmp5)
[1] 16533.27377 69.38894 104.01376 74.30957 34.89506 53.42207
[7] 15.16006 63.78695 33.21972 NA 18.26978 72.87095
[13] 133.01796 49.57443 66.61316 43.39931 78.83912 64.04114
[19] 49.86647 105.98486
> colSd(tmp5)
[1] 128.581779 8.330002 10.198714 8.620300 5.907204 7.309040
[7] 3.893592 7.986673 5.763655 NA 4.274316 8.536448
[13] 11.533341 7.040911 8.161688 6.587815 8.879140 8.002571
[19] 7.061620 10.294895
> colMax(tmp5)
[1] 473.53628 85.80689 83.86949 88.16632 77.78591 80.38661 76.66692
[8] 79.64810 82.40429 NA 76.19193 90.47666 92.64781 77.94739
[15] 82.07841 77.80338 85.87125 86.54254 79.31017 91.43643
> colMin(tmp5)
[1] 57.79595 58.57917 54.47547 57.04407 56.16488 55.80980 62.02136 54.38910
[9] 64.77587 NA 63.31363 57.73316 57.98204 54.46750 55.96660 59.43149
[17] 59.36992 59.67869 60.51280 57.17098
>
> Max(tmp5,na.rm=TRUE)
[1] 473.5363
> Min(tmp5,na.rm=TRUE)
[1] 54.3891
> mean(tmp5,na.rm=TRUE)
[1] 71.52349
> Sum(tmp5,na.rm=TRUE)
[1] 14233.17
> Var(tmp5,na.rm=TRUE)
[1] 881.911
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 89.73725 70.11865 70.00588 67.87043 69.68651 69.10518 71.06093 69.94240
[9] 68.08015 69.55160
> rowSums(tmp5,na.rm=TRUE)
[1] 1794.745 1402.373 1330.112 1357.409 1393.730 1382.104 1421.219 1398.848
[9] 1361.603 1391.032
> rowVars(tmp5,na.rm=TRUE)
[1] 8217.24169 44.40166 34.77470 70.58772 107.21898 54.77081
[7] 61.33131 35.41393 84.88415 84.87870
> rowSd(tmp5,na.rm=TRUE)
[1] 90.649003 6.663457 5.897008 8.401650 10.354660 7.400730 7.831431
[8] 5.950960 9.213260 9.212964
> rowMax(tmp5,na.rm=TRUE)
[1] 473.53628 80.29548 82.98963 92.64781 89.33946 90.47666 85.87125
[8] 79.31017 91.43643 88.16632
> rowMin(tmp5,na.rm=TRUE)
[1] 57.04407 59.30985 59.43149 54.38910 54.46750 56.87122 55.80980 57.19926
[9] 54.47547 55.96660
>
> colMeans(tmp5,na.rm=TRUE)
[1] 108.17714 71.98048 69.24573 70.24941 67.95051 70.11946 67.31418
[8] 66.45897 69.87140 70.83766 69.68957 70.84890 71.38298 65.97849
[15] 70.60462 67.79053 69.95409 72.62351 69.32358 69.99993
> colSums(tmp5,na.rm=TRUE)
[1] 1081.7714 719.8048 692.4573 702.4941 679.5051 701.1946 673.1418
[8] 664.5897 698.7140 637.5390 696.8957 708.4890 713.8298 659.7849
[15] 706.0462 677.9053 699.5409 726.2351 693.2358 699.9993
> colVars(tmp5,na.rm=TRUE)
[1] 16533.27377 69.38894 104.01376 74.30957 34.89506 53.42207
[7] 15.16006 63.78695 33.21972 115.39758 18.26978 72.87095
[13] 133.01796 49.57443 66.61316 43.39931 78.83912 64.04114
[19] 49.86647 105.98486
> colSd(tmp5,na.rm=TRUE)
[1] 128.581779 8.330002 10.198714 8.620300 5.907204 7.309040
[7] 3.893592 7.986673 5.763655 10.742326 4.274316 8.536448
[13] 11.533341 7.040911 8.161688 6.587815 8.879140 8.002571
[19] 7.061620 10.294895
> colMax(tmp5,na.rm=TRUE)
[1] 473.53628 85.80689 83.86949 88.16632 77.78591 80.38661 76.66692
[8] 79.64810 82.40429 87.36468 76.19193 90.47666 92.64781 77.94739
[15] 82.07841 77.80338 85.87125 86.54254 79.31017 91.43643
> colMin(tmp5,na.rm=TRUE)
[1] 57.79595 58.57917 54.47547 57.04407 56.16488 55.80980 62.02136 54.38910
[9] 64.77587 56.87122 63.31363 57.73316 57.98204 54.46750 55.96660 59.43149
[17] 59.36992 59.67869 60.51280 57.17098
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 89.73725 70.11865 NaN 67.87043 69.68651 69.10518 71.06093 69.94240
[9] 68.08015 69.55160
> rowSums(tmp5,na.rm=TRUE)
[1] 1794.745 1402.373 0.000 1357.409 1393.730 1382.104 1421.219 1398.848
[9] 1361.603 1391.032
> rowVars(tmp5,na.rm=TRUE)
[1] 8217.24169 44.40166 NA 70.58772 107.21898 54.77081
[7] 61.33131 35.41393 84.88415 84.87870
> rowSd(tmp5,na.rm=TRUE)
[1] 90.649003 6.663457 NA 8.401650 10.354660 7.400730 7.831431
[8] 5.950960 9.213260 9.212964
> rowMax(tmp5,na.rm=TRUE)
[1] 473.53628 80.29548 NA 92.64781 89.33946 90.47666 85.87125
[8] 79.31017 91.43643 88.16632
> rowMin(tmp5,na.rm=TRUE)
[1] 57.04407 59.30985 NA 54.38910 54.46750 56.87122 55.80980 57.19926
[9] 54.47547 55.96660
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 110.97575 71.96613 69.09460 70.89825 68.00212 70.49158 67.24427
[8] 67.04249 70.03058 NaN 69.23646 70.57707 71.62539 66.28575
[15] 70.17188 68.71931 69.77855 71.86881 68.69953 70.12736
> colSums(tmp5,na.rm=TRUE)
[1] 998.7818 647.6951 621.8514 638.0842 612.0191 634.4242 605.1984 603.3824
[9] 630.2752 0.0000 623.1282 635.1936 644.6285 596.5718 631.5469 618.4738
[17] 628.0069 646.8193 618.2958 631.1463
> colVars(tmp5,na.rm=TRUE)
[1] 18511.82040 78.06024 116.75856 78.86219 39.22697 58.54205
[7] 17.00009 67.92974 37.08714 NA 18.24385 81.14852
[13] 148.98415 54.70910 72.83308 39.11958 88.34733 65.63871
[19] 51.71868 119.05026
> colSd(tmp5,na.rm=TRUE)
[1] 136.058151 8.835171 10.805487 8.880439 6.263144 7.651277
[7] 4.123116 8.241950 6.089921 NA 4.271282 9.008248
[13] 12.205906 7.396560 8.534230 6.254565 9.399326 8.101772
[19] 7.191570 10.911016
> colMax(tmp5,na.rm=TRUE)
[1] 473.53628 85.80689 83.86949 88.16632 77.78591 80.38661 76.66692
[8] 79.64810 82.40429 -Inf 76.19193 90.47666 92.64781 77.94739
[15] 82.07841 77.80338 85.87125 86.54254 79.31017 91.43643
> colMin(tmp5,na.rm=TRUE)
[1] 57.79595 58.57917 54.47547 57.04407 56.16488 55.80980 62.02136 54.38910
[9] 64.77587 Inf 63.31363 57.73316 57.98204 54.46750 55.96660 60.18725
[17] 59.36992 59.67869 60.51280 57.17098
>
>
>
>
> 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] 310.9031 187.7499 276.4035 167.5056 260.2815 200.3063 415.4608 103.6307
[9] 163.1533 363.2345
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 310.9031 187.7499 276.4035 167.5056 260.2815 200.3063 415.4608 103.6307
[9] 163.1533 363.2345
>
>
>
> 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] 0.000000e+00 8.526513e-14 2.842171e-14 -1.989520e-13 1.705303e-13
[6] 5.684342e-14 -8.526513e-14 5.684342e-14 0.000000e+00 -8.526513e-14
[11] 0.000000e+00 8.526513e-14 0.000000e+00 5.684342e-14 2.842171e-14
[16] 1.136868e-13 2.842171e-14 -1.136868e-13 0.000000e+00 0.000000e+00
>
>
>
>
>
>
>
>
>
>
> ## 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)
+ }
1 7
3 9
7 5
7 10
2 3
1 5
1 6
1 4
2 3
10 8
3 20
8 9
9 19
3 10
9 12
6 2
5 8
10 20
1 8
7 18
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] 2.838848
> Min(tmp)
[1] -2.333339
> mean(tmp)
[1] 0.1279512
> Sum(tmp)
[1] 12.79512
> Var(tmp)
[1] 1.324883
>
> rowMeans(tmp)
[1] 0.1279512
> rowSums(tmp)
[1] 12.79512
> rowVars(tmp)
[1] 1.324883
> rowSd(tmp)
[1] 1.151036
> rowMax(tmp)
[1] 2.838848
> rowMin(tmp)
[1] -2.333339
>
> colMeans(tmp)
[1] 0.34439970 -0.50310339 0.80135119 0.90760996 2.63937114 -1.19144164
[7] -0.26568177 -2.01100998 -1.89943934 -1.32234022 0.15982975 -2.32171283
[13] 1.47041815 0.99146671 -0.82906211 0.06969365 -0.96571277 -0.25266348
[19] -0.97381343 0.88672380 -1.36878232 -0.51018611 2.33739225 -1.37773009
[25] -0.31178684 -1.01673090 -1.04647940 -0.21597792 1.32314464 -0.31199180
[31] 0.78140367 -0.09994701 -1.16060306 1.91990257 -0.76093852 0.13491258
[37] -0.27826981 1.08687710 1.56287545 1.28194805 -0.16983671 0.94607708
[43] -0.31278542 1.61390447 0.71102415 -2.33333918 -0.50033264 1.40522227
[49] 0.20513274 -0.41037541 0.20845461 -0.56133185 1.06965780 0.76626386
[55] 1.53239520 1.82499866 -0.04158603 1.09269421 0.20079901 0.28553737
[61] 2.83884848 1.95302298 -1.60511925 0.97765111 0.15053480 0.07632675
[67] 0.71644943 -0.78335428 -0.91897832 0.46918768 0.13001130 -0.25455345
[73] 0.14042525 2.28957217 -0.76840317 1.45249568 0.64418261 0.14558554
[79] 0.46443395 1.90620270 0.11821520 -0.23218870 1.72804734 0.77292047
[85] -1.21676922 0.64173658 -1.76108908 1.85450215 -1.99739526 0.93908787
[91] -0.57647006 1.12765729 -0.04587682 1.05426564 -0.41407137 -0.71989996
[97] -1.06854528 -0.59219808 -1.68799519 -0.38982853
> colSums(tmp)
[1] 0.34439970 -0.50310339 0.80135119 0.90760996 2.63937114 -1.19144164
[7] -0.26568177 -2.01100998 -1.89943934 -1.32234022 0.15982975 -2.32171283
[13] 1.47041815 0.99146671 -0.82906211 0.06969365 -0.96571277 -0.25266348
[19] -0.97381343 0.88672380 -1.36878232 -0.51018611 2.33739225 -1.37773009
[25] -0.31178684 -1.01673090 -1.04647940 -0.21597792 1.32314464 -0.31199180
[31] 0.78140367 -0.09994701 -1.16060306 1.91990257 -0.76093852 0.13491258
[37] -0.27826981 1.08687710 1.56287545 1.28194805 -0.16983671 0.94607708
[43] -0.31278542 1.61390447 0.71102415 -2.33333918 -0.50033264 1.40522227
[49] 0.20513274 -0.41037541 0.20845461 -0.56133185 1.06965780 0.76626386
[55] 1.53239520 1.82499866 -0.04158603 1.09269421 0.20079901 0.28553737
[61] 2.83884848 1.95302298 -1.60511925 0.97765111 0.15053480 0.07632675
[67] 0.71644943 -0.78335428 -0.91897832 0.46918768 0.13001130 -0.25455345
[73] 0.14042525 2.28957217 -0.76840317 1.45249568 0.64418261 0.14558554
[79] 0.46443395 1.90620270 0.11821520 -0.23218870 1.72804734 0.77292047
[85] -1.21676922 0.64173658 -1.76108908 1.85450215 -1.99739526 0.93908787
[91] -0.57647006 1.12765729 -0.04587682 1.05426564 -0.41407137 -0.71989996
[97] -1.06854528 -0.59219808 -1.68799519 -0.38982853
> 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] 0.34439970 -0.50310339 0.80135119 0.90760996 2.63937114 -1.19144164
[7] -0.26568177 -2.01100998 -1.89943934 -1.32234022 0.15982975 -2.32171283
[13] 1.47041815 0.99146671 -0.82906211 0.06969365 -0.96571277 -0.25266348
[19] -0.97381343 0.88672380 -1.36878232 -0.51018611 2.33739225 -1.37773009
[25] -0.31178684 -1.01673090 -1.04647940 -0.21597792 1.32314464 -0.31199180
[31] 0.78140367 -0.09994701 -1.16060306 1.91990257 -0.76093852 0.13491258
[37] -0.27826981 1.08687710 1.56287545 1.28194805 -0.16983671 0.94607708
[43] -0.31278542 1.61390447 0.71102415 -2.33333918 -0.50033264 1.40522227
[49] 0.20513274 -0.41037541 0.20845461 -0.56133185 1.06965780 0.76626386
[55] 1.53239520 1.82499866 -0.04158603 1.09269421 0.20079901 0.28553737
[61] 2.83884848 1.95302298 -1.60511925 0.97765111 0.15053480 0.07632675
[67] 0.71644943 -0.78335428 -0.91897832 0.46918768 0.13001130 -0.25455345
[73] 0.14042525 2.28957217 -0.76840317 1.45249568 0.64418261 0.14558554
[79] 0.46443395 1.90620270 0.11821520 -0.23218870 1.72804734 0.77292047
[85] -1.21676922 0.64173658 -1.76108908 1.85450215 -1.99739526 0.93908787
[91] -0.57647006 1.12765729 -0.04587682 1.05426564 -0.41407137 -0.71989996
[97] -1.06854528 -0.59219808 -1.68799519 -0.38982853
> colMin(tmp)
[1] 0.34439970 -0.50310339 0.80135119 0.90760996 2.63937114 -1.19144164
[7] -0.26568177 -2.01100998 -1.89943934 -1.32234022 0.15982975 -2.32171283
[13] 1.47041815 0.99146671 -0.82906211 0.06969365 -0.96571277 -0.25266348
[19] -0.97381343 0.88672380 -1.36878232 -0.51018611 2.33739225 -1.37773009
[25] -0.31178684 -1.01673090 -1.04647940 -0.21597792 1.32314464 -0.31199180
[31] 0.78140367 -0.09994701 -1.16060306 1.91990257 -0.76093852 0.13491258
[37] -0.27826981 1.08687710 1.56287545 1.28194805 -0.16983671 0.94607708
[43] -0.31278542 1.61390447 0.71102415 -2.33333918 -0.50033264 1.40522227
[49] 0.20513274 -0.41037541 0.20845461 -0.56133185 1.06965780 0.76626386
[55] 1.53239520 1.82499866 -0.04158603 1.09269421 0.20079901 0.28553737
[61] 2.83884848 1.95302298 -1.60511925 0.97765111 0.15053480 0.07632675
[67] 0.71644943 -0.78335428 -0.91897832 0.46918768 0.13001130 -0.25455345
[73] 0.14042525 2.28957217 -0.76840317 1.45249568 0.64418261 0.14558554
[79] 0.46443395 1.90620270 0.11821520 -0.23218870 1.72804734 0.77292047
[85] -1.21676922 0.64173658 -1.76108908 1.85450215 -1.99739526 0.93908787
[91] -0.57647006 1.12765729 -0.04587682 1.05426564 -0.41407137 -0.71989996
[97] -1.06854528 -0.59219808 -1.68799519 -0.38982853
> colMedians(tmp)
[1] 0.34439970 -0.50310339 0.80135119 0.90760996 2.63937114 -1.19144164
[7] -0.26568177 -2.01100998 -1.89943934 -1.32234022 0.15982975 -2.32171283
[13] 1.47041815 0.99146671 -0.82906211 0.06969365 -0.96571277 -0.25266348
[19] -0.97381343 0.88672380 -1.36878232 -0.51018611 2.33739225 -1.37773009
[25] -0.31178684 -1.01673090 -1.04647940 -0.21597792 1.32314464 -0.31199180
[31] 0.78140367 -0.09994701 -1.16060306 1.91990257 -0.76093852 0.13491258
[37] -0.27826981 1.08687710 1.56287545 1.28194805 -0.16983671 0.94607708
[43] -0.31278542 1.61390447 0.71102415 -2.33333918 -0.50033264 1.40522227
[49] 0.20513274 -0.41037541 0.20845461 -0.56133185 1.06965780 0.76626386
[55] 1.53239520 1.82499866 -0.04158603 1.09269421 0.20079901 0.28553737
[61] 2.83884848 1.95302298 -1.60511925 0.97765111 0.15053480 0.07632675
[67] 0.71644943 -0.78335428 -0.91897832 0.46918768 0.13001130 -0.25455345
[73] 0.14042525 2.28957217 -0.76840317 1.45249568 0.64418261 0.14558554
[79] 0.46443395 1.90620270 0.11821520 -0.23218870 1.72804734 0.77292047
[85] -1.21676922 0.64173658 -1.76108908 1.85450215 -1.99739526 0.93908787
[91] -0.57647006 1.12765729 -0.04587682 1.05426564 -0.41407137 -0.71989996
[97] -1.06854528 -0.59219808 -1.68799519 -0.38982853
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.3443997 -0.5031034 0.8013512 0.90761 2.639371 -1.191442 -0.2656818
[2,] 0.3443997 -0.5031034 0.8013512 0.90761 2.639371 -1.191442 -0.2656818
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -2.01101 -1.899439 -1.32234 0.1598297 -2.321713 1.470418 0.9914667
[2,] -2.01101 -1.899439 -1.32234 0.1598297 -2.321713 1.470418 0.9914667
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -0.8290621 0.06969365 -0.9657128 -0.2526635 -0.9738134 0.8867238 -1.368782
[2,] -0.8290621 0.06969365 -0.9657128 -0.2526635 -0.9738134 0.8867238 -1.368782
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.5101861 2.337392 -1.37773 -0.3117868 -1.016731 -1.046479 -0.2159779
[2,] -0.5101861 2.337392 -1.37773 -0.3117868 -1.016731 -1.046479 -0.2159779
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 1.323145 -0.3119918 0.7814037 -0.09994701 -1.160603 1.919903 -0.7609385
[2,] 1.323145 -0.3119918 0.7814037 -0.09994701 -1.160603 1.919903 -0.7609385
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.1349126 -0.2782698 1.086877 1.562875 1.281948 -0.1698367 0.9460771
[2,] 0.1349126 -0.2782698 1.086877 1.562875 1.281948 -0.1698367 0.9460771
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.3127854 1.613904 0.7110242 -2.333339 -0.5003326 1.405222 0.2051327
[2,] -0.3127854 1.613904 0.7110242 -2.333339 -0.5003326 1.405222 0.2051327
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -0.4103754 0.2084546 -0.5613319 1.069658 0.7662639 1.532395 1.824999
[2,] -0.4103754 0.2084546 -0.5613319 1.069658 0.7662639 1.532395 1.824999
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -0.04158603 1.092694 0.200799 0.2855374 2.838848 1.953023 -1.605119
[2,] -0.04158603 1.092694 0.200799 0.2855374 2.838848 1.953023 -1.605119
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.9776511 0.1505348 0.07632675 0.7164494 -0.7833543 -0.9189783 0.4691877
[2,] 0.9776511 0.1505348 0.07632675 0.7164494 -0.7833543 -0.9189783 0.4691877
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 0.1300113 -0.2545534 0.1404253 2.289572 -0.7684032 1.452496 0.6441826
[2,] 0.1300113 -0.2545534 0.1404253 2.289572 -0.7684032 1.452496 0.6441826
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 0.1455855 0.464434 1.906203 0.1182152 -0.2321887 1.728047 0.7729205
[2,] 0.1455855 0.464434 1.906203 0.1182152 -0.2321887 1.728047 0.7729205
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -1.216769 0.6417366 -1.761089 1.854502 -1.997395 0.9390879 -0.5764701
[2,] -1.216769 0.6417366 -1.761089 1.854502 -1.997395 0.9390879 -0.5764701
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 1.127657 -0.04587682 1.054266 -0.4140714 -0.7199 -1.068545 -0.5921981
[2,] 1.127657 -0.04587682 1.054266 -0.4140714 -0.7199 -1.068545 -0.5921981
[,99] [,100]
[1,] -1.687995 -0.3898285
[2,] -1.687995 -0.3898285
>
>
> Max(tmp2)
[1] 2.25327
> Min(tmp2)
[1] -2.187369
> mean(tmp2)
[1] 0.02308285
> Sum(tmp2)
[1] 2.308285
> Var(tmp2)
[1] 0.8732222
>
> rowMeans(tmp2)
[1] 0.78719905 -1.17147324 0.56855304 0.99376703 0.19135240 -0.93817816
[7] 0.38457338 -1.42891150 1.24529530 0.91409289 1.05558138 -2.18736874
[13] 0.58097493 -0.50509158 -0.01596164 -1.09007078 -0.64478388 0.19538314
[19] -0.21569776 2.14783268 -0.05919088 -0.99017925 2.25326970 -0.95978612
[25] 0.25238438 -0.65971630 -0.05351659 -1.24530106 0.78073203 0.13459247
[31] 0.17959651 0.52836984 1.75774356 1.16805994 0.70344996 0.15906463
[37] 0.85101524 0.05274414 -1.52678577 -1.08589653 -0.50358751 0.61190425
[43] -0.66693416 1.56601267 0.67391540 -0.65465611 -0.86331958 -0.40507116
[49] 1.38976762 0.87162609 0.36504630 -0.57766911 -0.83822190 1.21563017
[55] 1.13125579 0.14002646 -1.09598777 -1.07006019 1.13511336 -0.27033715
[61] 0.21295492 0.83518836 -1.14263102 -0.26977180 0.12222695 0.83838709
[67] -1.21690286 0.21687840 -0.18548135 -0.89282561 0.86088373 0.14702827
[73] 0.55316511 -0.60766770 0.22030395 1.21379915 -0.48874489 -0.42851270
[79] -0.29934133 -0.45058861 -0.48240726 -1.03622311 -0.96575172 -0.99063698
[85] -1.10932337 1.18933023 -0.61015194 -1.68224197 0.34673321 -1.70684109
[91] -0.16481467 1.20167373 0.68943721 -0.69029089 1.84267743 -0.15954312
[97] 1.17632845 1.26757691 -0.47628405 0.16851895
> rowSums(tmp2)
[1] 0.78719905 -1.17147324 0.56855304 0.99376703 0.19135240 -0.93817816
[7] 0.38457338 -1.42891150 1.24529530 0.91409289 1.05558138 -2.18736874
[13] 0.58097493 -0.50509158 -0.01596164 -1.09007078 -0.64478388 0.19538314
[19] -0.21569776 2.14783268 -0.05919088 -0.99017925 2.25326970 -0.95978612
[25] 0.25238438 -0.65971630 -0.05351659 -1.24530106 0.78073203 0.13459247
[31] 0.17959651 0.52836984 1.75774356 1.16805994 0.70344996 0.15906463
[37] 0.85101524 0.05274414 -1.52678577 -1.08589653 -0.50358751 0.61190425
[43] -0.66693416 1.56601267 0.67391540 -0.65465611 -0.86331958 -0.40507116
[49] 1.38976762 0.87162609 0.36504630 -0.57766911 -0.83822190 1.21563017
[55] 1.13125579 0.14002646 -1.09598777 -1.07006019 1.13511336 -0.27033715
[61] 0.21295492 0.83518836 -1.14263102 -0.26977180 0.12222695 0.83838709
[67] -1.21690286 0.21687840 -0.18548135 -0.89282561 0.86088373 0.14702827
[73] 0.55316511 -0.60766770 0.22030395 1.21379915 -0.48874489 -0.42851270
[79] -0.29934133 -0.45058861 -0.48240726 -1.03622311 -0.96575172 -0.99063698
[85] -1.10932337 1.18933023 -0.61015194 -1.68224197 0.34673321 -1.70684109
[91] -0.16481467 1.20167373 0.68943721 -0.69029089 1.84267743 -0.15954312
[97] 1.17632845 1.26757691 -0.47628405 0.16851895
> 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] 0.78719905 -1.17147324 0.56855304 0.99376703 0.19135240 -0.93817816
[7] 0.38457338 -1.42891150 1.24529530 0.91409289 1.05558138 -2.18736874
[13] 0.58097493 -0.50509158 -0.01596164 -1.09007078 -0.64478388 0.19538314
[19] -0.21569776 2.14783268 -0.05919088 -0.99017925 2.25326970 -0.95978612
[25] 0.25238438 -0.65971630 -0.05351659 -1.24530106 0.78073203 0.13459247
[31] 0.17959651 0.52836984 1.75774356 1.16805994 0.70344996 0.15906463
[37] 0.85101524 0.05274414 -1.52678577 -1.08589653 -0.50358751 0.61190425
[43] -0.66693416 1.56601267 0.67391540 -0.65465611 -0.86331958 -0.40507116
[49] 1.38976762 0.87162609 0.36504630 -0.57766911 -0.83822190 1.21563017
[55] 1.13125579 0.14002646 -1.09598777 -1.07006019 1.13511336 -0.27033715
[61] 0.21295492 0.83518836 -1.14263102 -0.26977180 0.12222695 0.83838709
[67] -1.21690286 0.21687840 -0.18548135 -0.89282561 0.86088373 0.14702827
[73] 0.55316511 -0.60766770 0.22030395 1.21379915 -0.48874489 -0.42851270
[79] -0.29934133 -0.45058861 -0.48240726 -1.03622311 -0.96575172 -0.99063698
[85] -1.10932337 1.18933023 -0.61015194 -1.68224197 0.34673321 -1.70684109
[91] -0.16481467 1.20167373 0.68943721 -0.69029089 1.84267743 -0.15954312
[97] 1.17632845 1.26757691 -0.47628405 0.16851895
> rowMin(tmp2)
[1] 0.78719905 -1.17147324 0.56855304 0.99376703 0.19135240 -0.93817816
[7] 0.38457338 -1.42891150 1.24529530 0.91409289 1.05558138 -2.18736874
[13] 0.58097493 -0.50509158 -0.01596164 -1.09007078 -0.64478388 0.19538314
[19] -0.21569776 2.14783268 -0.05919088 -0.99017925 2.25326970 -0.95978612
[25] 0.25238438 -0.65971630 -0.05351659 -1.24530106 0.78073203 0.13459247
[31] 0.17959651 0.52836984 1.75774356 1.16805994 0.70344996 0.15906463
[37] 0.85101524 0.05274414 -1.52678577 -1.08589653 -0.50358751 0.61190425
[43] -0.66693416 1.56601267 0.67391540 -0.65465611 -0.86331958 -0.40507116
[49] 1.38976762 0.87162609 0.36504630 -0.57766911 -0.83822190 1.21563017
[55] 1.13125579 0.14002646 -1.09598777 -1.07006019 1.13511336 -0.27033715
[61] 0.21295492 0.83518836 -1.14263102 -0.26977180 0.12222695 0.83838709
[67] -1.21690286 0.21687840 -0.18548135 -0.89282561 0.86088373 0.14702827
[73] 0.55316511 -0.60766770 0.22030395 1.21379915 -0.48874489 -0.42851270
[79] -0.29934133 -0.45058861 -0.48240726 -1.03622311 -0.96575172 -0.99063698
[85] -1.10932337 1.18933023 -0.61015194 -1.68224197 0.34673321 -1.70684109
[91] -0.16481467 1.20167373 0.68943721 -0.69029089 1.84267743 -0.15954312
[97] 1.17632845 1.26757691 -0.47628405 0.16851895
>
> colMeans(tmp2)
[1] 0.02308285
> colSums(tmp2)
[1] 2.308285
> colVars(tmp2)
[1] 0.8732222
> colSd(tmp2)
[1] 0.9344636
> colMax(tmp2)
[1] 2.25327
> colMin(tmp2)
[1] -2.187369
> colMedians(tmp2)
[1] 0.08748555
> colRanges(tmp2)
[,1]
[1,] -2.187369
[2,] 2.253270
>
> 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] 2.3899135 0.5724590 2.9708960 -0.8756505 0.6682220 -0.9095832
[7] -0.6155334 -7.7771090 3.4568131 2.2599130
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.60583102
[2,] -0.69027339
[3,] -0.01695966
[4,] 0.95575498
[5,] 3.40841882
>
> rowApply(tmp,sum)
[1] 2.477503654 1.388992400 0.002507165 -2.050983363 1.789606308
[6] -1.667126426 -0.547285269 0.761430501 1.445080170 -1.459384724
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 7 8 5 9 10 4 4 2 4 1
[2,] 5 3 8 8 6 5 10 3 6 4
[3,] 2 7 6 6 5 8 6 8 10 8
[4,] 9 4 4 10 2 2 3 6 9 2
[5,] 8 10 7 1 9 6 1 1 8 5
[6,] 3 2 9 2 7 9 7 5 3 3
[7,] 4 9 1 3 4 3 9 10 5 6
[8,] 1 5 3 7 1 1 2 4 2 7
[9,] 6 1 10 5 8 7 5 7 7 10
[10,] 10 6 2 4 3 10 8 9 1 9
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 1.5444435 -1.7181585 -1.6357745 -0.3299123 -0.5393683 -4.1679858
[7] 3.0822250 -1.8256692 -1.8406631 1.2303483 2.0119718 -1.6001267
[13] -3.5011073 2.3338059 -1.5108883 -2.0889670 -0.4470630 -3.5798166
[19] 0.4085182 0.7578223
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.2771009
[2,] -0.3761432
[3,] 0.3824557
[4,] 0.9676712
[5,] 1.8475607
>
> rowApply(tmp,sum)
[1] -2.9808876 -3.7320658 -9.3938294 -0.1925472 2.8829643
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 18 15 5 8 19
[2,] 13 16 8 6 4
[3,] 9 17 10 10 3
[4,] 4 12 15 16 9
[5,] 10 7 6 19 10
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.9676712 0.1577678 -0.3924664 -0.96270426 -0.3608383 0.02085409
[2,] 0.3824557 0.7618877 0.8154927 0.05268613 -0.5578133 -2.63599795
[3,] -1.2771009 -0.8992795 -0.5809966 0.32352488 -1.2302236 0.41288884
[4,] -0.3761432 -0.5831963 -0.1444931 0.70533718 1.4611856 -0.60946448
[5,] 1.8475607 -1.1553381 -1.3333112 -0.44875627 0.1483213 -1.35626630
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 1.1004302 -2.1273122696 -0.11152970 -0.4037146 1.4348264 0.3859512
[2,] 1.4750835 -0.4047942940 1.19663167 1.8410013 -0.1272048 -1.1984572
[3,] 0.4874158 -1.3272531705 -1.87837660 1.0602776 -0.9141938 -0.6221531
[4,] 1.5578822 0.0006620617 -0.05461112 -0.7420825 0.9658084 -0.4383104
[5,] -1.5385867 2.0330284609 -0.99277738 -0.5251335 0.6527357 0.2728428
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.4558616 0.44766688 -0.6201289 -1.4881909 0.5260341 -1.63791498
[2,] -0.8432775 -0.83817839 -0.2646798 -1.5371381 -0.2914328 0.07726692
[3,] -2.8406130 0.01631446 -2.1369334 -0.2111579 0.1593149 0.97124070
[4,] -0.5979389 1.42903349 -0.1610649 0.1940608 0.2115400 -1.93645391
[5,] 1.2365837 1.27896951 1.6719188 0.9534590 -1.0525193 -1.05395537
[,19] [,20]
[1,] 0.95529543 -0.416723
[2,] -1.90032610 0.264729
[3,] 0.04563757 1.047837
[4,] 0.56029663 -1.634595
[5,] 0.74761465 1.496574
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 654 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 565 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 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 0.5703736 -1.837586 -0.07014745 1.048369 -0.5815251 -0.4674158 -0.8119541
col8 col9 col10 col11 col12 col13 col14
row1 -1.475427 -0.693162 -0.94371 -1.358652 -0.9280934 -0.6601939 -1.288403
col15 col16 col17 col18 col19 col20
row1 0.9263812 1.21276 -0.8336813 -0.8994359 0.9060116 -0.4009701
> tmp[,"col10"]
col10
row1 -0.9437100
row2 0.6911499
row3 0.4215545
row4 1.6309368
row5 0.8421802
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 0.5703736 -1.8375857 -0.07014745 1.0483686 -0.5815251 -0.4674158
row5 -0.1004228 -0.2069567 0.26095666 -0.2236117 1.4460379 0.9297905
col7 col8 col9 col10 col11 col12
row1 -0.8119541 -1.4754272 -0.693162 -0.9437100 -1.3586516 -0.9280934
row5 -2.1408964 0.7467463 1.166572 0.8421802 0.9345004 -1.1096843
col13 col14 col15 col16 col17 col18
row1 -0.6601939 -1.2884032 0.9263812 1.21275987 -0.8336813 -0.8994359
row5 -1.8355871 0.1323834 -0.3446477 -0.09767506 -1.9480821 0.3620029
col19 col20
row1 0.9060116 -0.4009701
row5 -2.3576987 -1.4325440
> tmp[,c("col6","col20")]
col6 col20
row1 -0.4674158 -0.4009701
row2 -1.0993389 0.2158561
row3 0.8432113 -0.8520471
row4 0.5240728 1.7578674
row5 0.9297905 -1.4325440
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.4674158 -0.4009701
row5 0.9297905 -1.4325440
>
>
>
>
> 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 51.13267 48.28676 48.73111 49.57162 50.72202 103.4456 49.86999 51.78693
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.78393 47.45268 50.90575 47.49857 47.8397 49.22541 50.56126 48.06228
col17 col18 col19 col20
row1 50.83119 48.96951 50.01869 105.1098
> tmp[,"col10"]
col10
row1 47.45268
row2 30.66354
row3 31.75056
row4 29.75235
row5 48.97510
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 51.13267 48.28676 48.73111 49.57162 50.72202 103.4456 49.86999 51.78693
row5 50.13208 49.96209 49.00542 52.23649 49.58431 105.5884 49.69901 51.07494
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.78393 47.45268 50.90575 47.49857 47.8397 49.22541 50.56126 48.06228
row5 50.21316 48.97510 49.14828 50.16238 49.5212 50.84419 49.62744 50.45846
col17 col18 col19 col20
row1 50.83119 48.96951 50.01869 105.1098
row5 48.90296 49.95012 50.12894 105.5999
> tmp[,c("col6","col20")]
col6 col20
row1 103.44560 105.10983
row2 74.64740 74.44852
row3 75.40795 73.88471
row4 74.24548 75.23256
row5 105.58838 105.59987
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 103.4456 105.1098
row5 105.5884 105.5999
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 103.4456 105.1098
row5 105.5884 105.5999
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.7365561
[2,] 0.5343265
[3,] -0.2007881
[4,] -0.4508347
[5,] 1.1795831
> tmp[,c("col17","col7")]
col17 col7
[1,] 2.5422914 0.05869537
[2,] 0.9358422 0.97937914
[3,] -0.7307338 0.04374093
[4,] 0.7005390 0.86668592
[5,] -1.0568334 -0.84174320
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.3860972 0.7707754
[2,] -0.5080268 -0.9069586
[3,] 0.9526823 0.9263933
[4,] 0.1682416 0.3634027
[5,] -0.3807110 -1.0387400
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.3860972
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.3860972
[2,] -0.5080268
>
>
>
> 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] [,7]
row3 0.1704275 -0.5613262 -2.4815249 1.5152867 0.7938181 0.1847018 1.9225278
row1 -0.1859549 -2.0931427 0.4709032 0.1914951 -0.1090012 -0.8591785 0.5081302
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row3 0.4176263 0.4051509 -2.064808 -0.4305248 1.7254509 -0.3327988 0.8897191
row1 -0.1039924 -0.6775098 1.531704 0.4293067 0.7788134 0.4936417 -1.2092894
[,15] [,16] [,17] [,18] [,19] [,20]
row3 -0.8536477 0.508504 -0.3676630 -0.4335322 -0.4407061 0.5038567
row1 0.6638338 -0.733905 0.9812674 -0.5256779 1.7631995 -0.9836812
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.7865253 1.164161 -1.971526 -0.632742 -0.03290069 -0.5803871 0.0230741
[,8] [,9] [,10]
row2 -1.187392 1.810121 0.2716555
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -0.05376889 1.152586 -1.581651 1.54635 2.041915 0.1628128 0.1879411
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -1.222923 -0.298082 -0.9680419 -0.2174006 0.7711277 -1.786409 1.441308
[,15] [,16] [,17] [,18] [,19] [,20]
row5 0.04947766 -0.05555992 -1.08673 -1.407326 -1.662586 -1.231378
>
>
> 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: 0x5627498de2a0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM244d56410efae8"
[2] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM244d563ada009b"
[3] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM244d564ca45bef"
[4] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM244d5648b04dd2"
[5] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM244d5664ad8fe0"
[6] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM244d56de60028"
[7] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM244d566dd880e9"
[8] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM244d56b89a236"
[9] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM244d5620b13ca8"
[10] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM244d56536b4f52"
[11] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM244d561a0561ca"
[12] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM244d567cbcc4ad"
[13] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM244d562201eed6"
[14] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM244d567f6c1823"
[15] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BM244d56382489f9"
>
>
> ### 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: 0x562746d640e0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x562746d640e0>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x562746d640e0>
> rowMedians(tmp)
[1] -0.4849866687 0.6639600142 0.4319543142 0.1617090711 0.1151112756
[6] -0.7492641496 0.1657912225 0.3431792863 -0.9329098318 -0.3208375836
[11] 0.0678575080 -0.1467323359 -0.2520785767 -0.1038912948 -0.0326170719
[16] 0.3080770854 0.4007075131 0.1278985987 -0.6722724348 -0.0611377054
[21] 0.0620078527 -0.1364758775 -0.1657107607 0.3159978602 0.4931284039
[26] 0.1206449840 -0.1350023180 -0.2164237408 0.2733279569 -0.6186428573
[31] -0.7189033528 0.4094982505 -0.0365799977 -0.0758293278 -0.3772932587
[36] 0.4101562980 -0.2288027328 -0.1328739980 0.5306543417 -0.1664605838
[41] 0.4065898796 0.3964684274 0.2791747362 -0.2497512410 -0.3724229474
[46] 0.3404012625 -0.0894536029 -0.3915529807 -0.1631911376 0.3220827986
[51] -0.1154998764 0.2476621390 0.0497507063 -0.3178350001 -0.3677828792
[56] -0.0848171138 0.2713723374 0.2998213360 0.1028643353 0.1628787899
[61] -0.2484742287 -0.0331572596 -0.0747246041 0.0795099749 -0.1291984016
[66] 0.1957114264 -0.1563552180 -0.0659683357 0.1090960393 -0.2309273632
[71] 0.6260048746 0.3206725514 0.1655666625 0.5551387367 0.4687608918
[76] 0.0544781384 0.5312117400 0.1361623549 0.3899454261 -0.0411583998
[81] 0.0431740206 0.2275556912 0.2903610788 0.2688157175 0.1124221665
[86] -0.0381240794 0.0067251777 0.0824109328 -0.0200184165 -0.1355174711
[91] 0.2213000682 -0.5613156886 0.4088025754 0.2879344451 -0.2673595713
[96] 0.1457778752 -0.0801715203 -0.2831613799 0.3280557983 0.3236009201
[101] -0.4340321691 -0.2033579732 -0.1744259541 0.0945876117 -0.1170595783
[106] 0.0163358840 -0.1319460455 -0.1316211008 -0.1237206212 -0.0566056219
[111] 0.1661210030 0.2848435326 0.1390594729 -0.0507382588 0.1639247558
[116] -0.0847065115 -0.0198171579 -0.0657042511 0.2052533355 -0.3519695643
[121] -0.3085132663 -0.0914124976 0.5539608918 -0.0137503861 -0.1561600780
[126] -0.1889024594 0.2676211223 -0.1399116435 0.1109516222 -0.0748984100
[131] -0.3130645034 -0.3039747140 0.4288158233 -0.1759742511 -0.2821204848
[136] -0.0657530660 -0.0009431537 -0.0206361544 -0.4030043104 -0.3569731905
[141] -0.3416215813 -0.3190084602 -0.3315398959 -0.1727589125 0.5761503166
[146] -0.1197414857 0.0772233956 0.2869075494 -0.9910348256 0.0758191508
[151] 0.4654107831 -0.0220275558 0.3268074001 0.1309991538 0.0606209167
[156] 0.1524571970 0.2012452792 0.4842707928 -0.2654959319 -0.0493394260
[161] -0.2285814247 -0.1637607640 -0.1420707723 0.2031926839 0.2870653148
[166] 0.0532740032 0.0770648777 0.4668677765 0.0696730021 -0.1670952096
[171] 0.1803039853 0.3240847508 0.3566799077 0.0002643209 -0.1085976817
[176] -0.0482743678 -0.0038531745 -0.4400524221 -0.2252488660 -0.5050275862
[181] 0.1900468496 -0.2299529807 -0.1595652646 -0.3147436142 0.7539593191
[186] 0.1995257419 -0.6043676760 0.4768848228 0.2810731679 -0.1562857724
[191] 0.1697929606 0.0011737908 -0.0376224065 0.0445736712 -0.4166964822
[196] 0.1413589918 -0.0502096453 0.0090370809 0.0574324618 -0.2580711133
[201] -0.2066080987 -0.1279911435 0.1191044241 0.0773198506 0.1093870691
[206] -0.1577153305 -0.6484624958 0.1705106597 0.3057783700 -0.1801191250
[211] -0.5511931934 -0.3723949292 0.4889571687 0.1062042159 0.4281475589
[216] 0.3334392021 0.3388760079 0.2703079653 -0.2347797614 0.2678826803
[221] 0.8492442162 -0.5128808771 0.3850426650 -0.0659285071 0.2211076286
[226] 0.0397983214 -0.2618300787 0.3531812634 -0.0898530207 -0.0721911438
>
> proc.time()
user system elapsed
1.251 0.673 1.923
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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: 0x55d5d69d56b0>
> .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: 0x55d5d69d56b0>
> .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: 0x55d5d69d56b0>
> .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: 0x55d5d69d56b0>
> 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: 0x55d5d6ac1990>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55d5d6ac1990>
> .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: 0x55d5d6ac1990>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55d5d6ac1990>
> .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: 0x55d5d6ac1990>
> 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: 0x55d5d69c9f20>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55d5d69c9f20>
> .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: 0x55d5d69c9f20>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x55d5d69c9f20>
> .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: 0x55d5d69c9f20>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x55d5d69c9f20>
> .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: 0x55d5d69c9f20>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x55d5d69c9f20>
> .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: 0x55d5d69c9f20>
> 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: 0x55d5d5384650>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x55d5d5384650>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55d5d5384650>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55d5d5384650>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile244dfc1765ec7c" "BufferedMatrixFile244dfc4934d195"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile244dfc1765ec7c" "BufferedMatrixFile244dfc4934d195"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x55d5d5768080>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55d5d5768080>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x55d5d5768080>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x55d5d5768080>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x55d5d5768080>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x55d5d5768080>
> .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: 0x55d5d63c79e0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55d5d63c79e0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x55d5d63c79e0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x55d5d63c79e0>
> 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: 0x55d5d640bcc0>
> .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: 0x55d5d640bcc0>
> rm(P)
>
> proc.time()
user system elapsed
0.298 0.009 0.295
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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Type 'license()' or 'licence()' for distribution details.
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Type 'demo()' for some demos, 'help()' for on-line help, or
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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
0.251 0.050 0.291