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 11:38 -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: /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: 2024-07-23 21:40:20 -0400 (Tue, 23 Jul 2024) |
| EndedAt: 2024-07-23 21:40:43 -0400 (Tue, 23 Jul 2024) |
| EllapsedTime: 23.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 4.4.1 (2024-06-14)
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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
0.267 0.036 0.292
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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 471777 25.2 1026220 54.9 643428 34.4
Vcells 871900 6.7 8388608 64.0 2046605 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] "Tue Jul 23 21:40:35 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 21:40:35 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: 0x55ccc6485950>
>
>
>
> 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 21:40:36 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 21:40:36 2024"
>
> ColMode(tmp2)
<pointer: 0x55ccc6485950>
>
>
>
> ### 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,] 98.8530191 0.3600860 2.3963401 1.7358329
[2,] 1.3982922 1.6787899 0.3708756 0.6372400
[3,] 0.9086362 -0.1385156 -0.2495464 0.3075734
[4,] -0.9946254 0.6772771 0.4392134 1.4282214
> 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 : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 98.8530191 0.3600860 2.3963401 1.7358329
[2,] 1.3982922 1.6787899 0.3708756 0.6372400
[3,] 0.9086362 0.1385156 0.2495464 0.3075734
[4,] 0.9946254 0.6772771 0.4392134 1.4282214
> 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 : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 9.9424856 0.6000717 1.5480117 1.3175101
[2,] 1.1824941 1.2956812 0.6089956 0.7982732
[3,] 0.9532241 0.3721769 0.4995462 0.5545930
[4,] 0.9973091 0.8229685 0.6627318 1.1950822
>
> 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 : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 223.27787 31.36080 42.87646 39.91093
[2,] 38.22323 39.63560 31.46083 33.61997
[3,] 35.44088 28.86028 30.24501 30.85350
[4,] 35.96772 33.90696 32.06653 38.37904
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x55ccc6244a80>
> exp(tmp5)
<pointer: 0x55ccc6244a80>
> log(tmp5,2)
<pointer: 0x55ccc6244a80>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 464.7236
> Min(tmp5)
[1] 52.6174
> mean(tmp5)
[1] 71.79483
> Sum(tmp5)
[1] 14358.97
> Var(tmp5)
[1] 849.8712
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 89.88497 70.42712 66.80960 69.85283 69.07419 75.14177 70.03763 69.22552
[9] 66.42941 71.06528
> rowSums(tmp5)
[1] 1797.699 1408.542 1336.192 1397.057 1381.484 1502.835 1400.753 1384.510
[9] 1328.588 1421.306
> rowVars(tmp5)
[1] 7872.78835 60.93974 81.35307 47.23754 79.87452 78.37503
[7] 77.05299 62.76688 40.63940 63.03305
> rowSd(tmp5)
[1] 88.728735 7.806391 9.019594 6.872957 8.937255 8.852968 8.777983
[8] 7.922555 6.374904 7.939335
> rowMax(tmp5)
[1] 464.72364 82.49631 87.39946 80.76140 89.02067 94.57419 87.80031
[8] 83.75477 82.71531 91.03857
> rowMin(tmp5)
[1] 56.97971 57.31727 52.61740 57.25219 53.93710 59.75255 56.95493 57.17138
[9] 54.82017 56.12810
>
> colMeans(tmp5)
[1] 112.42789 68.05148 68.81386 76.35838 68.68345 67.07115 72.07602
[8] 65.80292 68.73672 68.87609 67.87257 71.50847 69.85203 69.54757
[15] 72.16761 67.49513 71.29316 67.69939 69.37774 72.18501
> colSums(tmp5)
[1] 1124.2789 680.5148 688.1386 763.5838 686.8345 670.7115 720.7602
[8] 658.0292 687.3672 688.7609 678.7257 715.0847 698.5203 695.4757
[15] 721.6761 674.9513 712.9316 676.9939 693.7774 721.8501
> colVars(tmp5)
[1] 15345.02689 130.42544 83.79884 102.02073 58.92681 126.84205
[7] 58.35208 51.07853 53.38938 77.46141 109.35596 70.02356
[13] 36.01166 74.50323 64.04032 49.23523 66.82370 84.94399
[19] 45.12417 52.48569
> colSd(tmp5)
[1] 123.875045 11.420396 9.154171 10.100531 7.676380 11.262418
[7] 7.638853 7.146925 7.306804 8.801216 10.457340 8.368008
[13] 6.000972 8.631526 8.002520 7.016782 8.174576 9.216506
[19] 6.717452 7.244701
> colMax(tmp5)
[1] 464.72364 91.65331 89.24173 94.57419 79.17231 91.03857 86.98742
[8] 77.82014 80.52176 87.39946 88.65805 81.85452 81.33481 84.63584
[15] 87.80031 83.75477 87.34352 80.06691 81.73238 83.98742
> colMin(tmp5)
[1] 64.23306 56.12810 53.93710 64.21753 57.73976 55.30094 65.21858 56.95493
[9] 58.11599 57.15662 52.61740 60.45935 64.16124 54.82017 63.27017 56.97971
[17] 61.09383 56.23241 61.12879 60.00047
>
>
> ### 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] 89.88497 70.42712 66.80960 69.85283 NA 75.14177 70.03763 69.22552
[9] 66.42941 71.06528
> rowSums(tmp5)
[1] 1797.699 1408.542 1336.192 1397.057 NA 1502.835 1400.753 1384.510
[9] 1328.588 1421.306
> rowVars(tmp5)
[1] 7872.78835 60.93974 81.35307 47.23754 84.31093 78.37503
[7] 77.05299 62.76688 40.63940 63.03305
> rowSd(tmp5)
[1] 88.728735 7.806391 9.019594 6.872957 9.182099 8.852968 8.777983
[8] 7.922555 6.374904 7.939335
> rowMax(tmp5)
[1] 464.72364 82.49631 87.39946 80.76140 NA 94.57419 87.80031
[8] 83.75477 82.71531 91.03857
> rowMin(tmp5)
[1] 56.97971 57.31727 52.61740 57.25219 NA 59.75255 56.95493 57.17138
[9] 54.82017 56.12810
>
> colMeans(tmp5)
[1] 112.42789 68.05148 68.81386 76.35838 68.68345 67.07115 72.07602
[8] 65.80292 68.73672 68.87609 67.87257 NA 69.85203 69.54757
[15] 72.16761 67.49513 71.29316 67.69939 69.37774 72.18501
> colSums(tmp5)
[1] 1124.2789 680.5148 688.1386 763.5838 686.8345 670.7115 720.7602
[8] 658.0292 687.3672 688.7609 678.7257 NA 698.5203 695.4757
[15] 721.6761 674.9513 712.9316 676.9939 693.7774 721.8501
> colVars(tmp5)
[1] 15345.02689 130.42544 83.79884 102.02073 58.92681 126.84205
[7] 58.35208 51.07853 53.38938 77.46141 109.35596 NA
[13] 36.01166 74.50323 64.04032 49.23523 66.82370 84.94399
[19] 45.12417 52.48569
> colSd(tmp5)
[1] 123.875045 11.420396 9.154171 10.100531 7.676380 11.262418
[7] 7.638853 7.146925 7.306804 8.801216 10.457340 NA
[13] 6.000972 8.631526 8.002520 7.016782 8.174576 9.216506
[19] 6.717452 7.244701
> colMax(tmp5)
[1] 464.72364 91.65331 89.24173 94.57419 79.17231 91.03857 86.98742
[8] 77.82014 80.52176 87.39946 88.65805 NA 81.33481 84.63584
[15] 87.80031 83.75477 87.34352 80.06691 81.73238 83.98742
> colMin(tmp5)
[1] 64.23306 56.12810 53.93710 64.21753 57.73976 55.30094 65.21858 56.95493
[9] 58.11599 57.15662 52.61740 NA 64.16124 54.82017 63.27017 56.97971
[17] 61.09383 56.23241 61.12879 60.00047
>
> Max(tmp5,na.rm=TRUE)
[1] 464.7236
> Min(tmp5,na.rm=TRUE)
[1] 52.6174
> mean(tmp5,na.rm=TRUE)
[1] 71.80918
> Sum(tmp5,na.rm=TRUE)
[1] 14290.03
> Var(tmp5,na.rm=TRUE)
[1] 854.1221
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 89.88497 70.42712 66.80960 69.85283 69.08128 75.14177 70.03763 69.22552
[9] 66.42941 71.06528
> rowSums(tmp5,na.rm=TRUE)
[1] 1797.699 1408.542 1336.192 1397.057 1312.544 1502.835 1400.753 1384.510
[9] 1328.588 1421.306
> rowVars(tmp5,na.rm=TRUE)
[1] 7872.78835 60.93974 81.35307 47.23754 84.31093 78.37503
[7] 77.05299 62.76688 40.63940 63.03305
> rowSd(tmp5,na.rm=TRUE)
[1] 88.728735 7.806391 9.019594 6.872957 9.182099 8.852968 8.777983
[8] 7.922555 6.374904 7.939335
> rowMax(tmp5,na.rm=TRUE)
[1] 464.72364 82.49631 87.39946 80.76140 89.02067 94.57419 87.80031
[8] 83.75477 82.71531 91.03857
> rowMin(tmp5,na.rm=TRUE)
[1] 56.97971 57.31727 52.61740 57.25219 53.93710 59.75255 56.95493 57.17138
[9] 54.82017 56.12810
>
> colMeans(tmp5,na.rm=TRUE)
[1] 112.42789 68.05148 68.81386 76.35838 68.68345 67.07115 72.07602
[8] 65.80292 68.73672 68.87609 67.87257 71.79391 69.85203 69.54757
[15] 72.16761 67.49513 71.29316 67.69939 69.37774 72.18501
> colSums(tmp5,na.rm=TRUE)
[1] 1124.2789 680.5148 688.1386 763.5838 686.8345 670.7115 720.7602
[8] 658.0292 687.3672 688.7609 678.7257 646.1452 698.5203 695.4757
[15] 721.6761 674.9513 712.9316 676.9939 693.7774 721.8501
> colVars(tmp5,na.rm=TRUE)
[1] 15345.02689 130.42544 83.79884 102.02073 58.92681 126.84205
[7] 58.35208 51.07853 53.38938 77.46141 109.35596 77.85992
[13] 36.01166 74.50323 64.04032 49.23523 66.82370 84.94399
[19] 45.12417 52.48569
> colSd(tmp5,na.rm=TRUE)
[1] 123.875045 11.420396 9.154171 10.100531 7.676380 11.262418
[7] 7.638853 7.146925 7.306804 8.801216 10.457340 8.823827
[13] 6.000972 8.631526 8.002520 7.016782 8.174576 9.216506
[19] 6.717452 7.244701
> colMax(tmp5,na.rm=TRUE)
[1] 464.72364 91.65331 89.24173 94.57419 79.17231 91.03857 86.98742
[8] 77.82014 80.52176 87.39946 88.65805 81.85452 81.33481 84.63584
[15] 87.80031 83.75477 87.34352 80.06691 81.73238 83.98742
> colMin(tmp5,na.rm=TRUE)
[1] 64.23306 56.12810 53.93710 64.21753 57.73976 55.30094 65.21858 56.95493
[9] 58.11599 57.15662 52.61740 60.45935 64.16124 54.82017 63.27017 56.97971
[17] 61.09383 56.23241 61.12879 60.00047
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 89.88497 70.42712 66.80960 69.85283 NaN 75.14177 70.03763 69.22552
[9] 66.42941 71.06528
> rowSums(tmp5,na.rm=TRUE)
[1] 1797.699 1408.542 1336.192 1397.057 0.000 1502.835 1400.753 1384.510
[9] 1328.588 1421.306
> rowVars(tmp5,na.rm=TRUE)
[1] 7872.78835 60.93974 81.35307 47.23754 NA 78.37503
[7] 77.05299 62.76688 40.63940 63.03305
> rowSd(tmp5,na.rm=TRUE)
[1] 88.728735 7.806391 9.019594 6.872957 NA 8.852968 8.777983
[8] 7.922555 6.374904 7.939335
> rowMax(tmp5,na.rm=TRUE)
[1] 464.72364 82.49631 87.39946 80.76140 NA 94.57419 87.80031
[8] 83.75477 82.71531 91.03857
> rowMin(tmp5,na.rm=TRUE)
[1] 56.97971 57.31727 52.61740 57.25219 NA 59.75255 56.95493 57.17138
[9] 54.82017 56.12810
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 116.75283 67.57622 70.46683 74.95145 69.25602 67.49268 70.41920
[8] 65.23362 69.91680 68.28490 68.19173 NaN 69.87414 68.70245
[15] 71.58938 67.74684 71.93985 68.13112 70.08371 73.53885
> colSums(tmp5,na.rm=TRUE)
[1] 1050.7755 608.1860 634.2015 674.5631 623.3041 607.4341 633.7728
[8] 587.1026 629.2512 614.5641 613.7256 0.0000 628.8672 618.3220
[15] 644.3044 609.7215 647.4586 613.1801 630.7534 661.8497
> colVars(tmp5,na.rm=TRUE)
[1] 17052.72315 144.18758 63.53512 92.50474 62.60459 140.69833
[7] 34.76416 53.81715 44.39638 83.21208 121.87951 NA
[13] 40.50762 75.78105 68.28389 54.67690 70.47177 93.46505
[19] 45.15774 38.42652
> colSd(tmp5,na.rm=TRUE)
[1] 130.586076 12.007813 7.970892 9.617938 7.912306 11.861633
[7] 5.896114 7.336017 6.663061 9.122065 11.039905 NA
[13] 6.364560 8.705231 8.263407 7.394383 8.394746 9.667732
[19] 6.719951 6.198913
> colMax(tmp5,na.rm=TRUE)
[1] 464.72364 91.65331 89.24173 94.57419 79.17231 91.03857 81.83205
[8] 77.82014 80.52176 87.39946 88.65805 -Inf 81.33481 84.63584
[15] 87.80031 83.75477 87.34352 80.06691 81.73238 83.98742
> colMin(tmp5,na.rm=TRUE)
[1] 64.23306 56.12810 62.95102 64.21753 57.73976 55.30094 65.21858 56.95493
[9] 59.75255 57.15662 52.61740 Inf 64.16124 54.82017 63.27017 56.97971
[17] 61.09383 56.23241 61.12879 67.22317
>
>
>
>
> 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] 230.0722 211.9102 186.6564 122.9709 176.5092 205.5269 269.7991 132.7169
[9] 155.2684 164.3520
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 230.0722 211.9102 186.6564 122.9709 176.5092 205.5269 269.7991 132.7169
[9] 155.2684 164.3520
>
>
>
> 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] 5.684342e-14 -8.526513e-14 2.842171e-13 2.842171e-14 0.000000e+00
[6] 8.526513e-14 -1.421085e-14 0.000000e+00 5.684342e-14 0.000000e+00
[11] -5.684342e-14 1.421085e-14 5.684342e-14 -5.684342e-14 0.000000e+00
[16] -5.684342e-14 -3.552714e-14 0.000000e+00 -1.136868e-13 -2.557954e-13
>
>
>
>
>
>
>
>
>
>
> ## 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 9
7 4
3 10
10 20
10 17
9 19
4 8
3 7
1 13
5 19
1 10
2 20
4 8
7 3
1 4
1 5
6 15
8 4
8 15
7 5
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] 2.82747
> Min(tmp)
[1] -2.255158
> mean(tmp)
[1] 0.006883071
> Sum(tmp)
[1] 0.6883071
> Var(tmp)
[1] 1.169892
>
> rowMeans(tmp)
[1] 0.006883071
> rowSums(tmp)
[1] 0.6883071
> rowVars(tmp)
[1] 1.169892
> rowSd(tmp)
[1] 1.081616
> rowMax(tmp)
[1] 2.82747
> rowMin(tmp)
[1] -2.255158
>
> colMeans(tmp)
[1] -1.94945213 0.39189703 1.43780627 -1.39626751 1.06871468 2.82747025
[7] -0.42119140 0.49503923 -0.56440230 -0.17147989 -0.11332199 -0.62873957
[13] -1.12240925 0.85190337 -0.46593677 -0.50190095 -0.68429250 0.18244308
[19] 1.82695041 -0.98754554 -1.27708141 1.10908105 -2.23301063 0.48208871
[25] 1.08557090 1.11424241 -1.14235775 -1.10408440 0.50914517 0.11892653
[31] 1.91689287 -0.94200355 -0.90732974 -0.57611867 -0.14554280 -0.26670855
[37] 0.38202752 0.44268340 2.36244220 -1.10606461 -0.82754724 0.53687027
[43] 0.49085452 2.02500472 -1.74969477 1.07301452 -1.30481524 0.47916396
[49] 1.13579349 0.64956406 -0.72498938 -1.55217473 0.63470977 0.03457418
[55] 1.84255503 1.15279288 1.59471087 0.73980085 0.77321098 -1.59011095
[61] -0.01789707 0.63965088 -1.53225932 0.37377099 0.49848342 -0.02194668
[67] 0.29797176 1.05719650 -1.15344750 0.28478297 -1.12421311 -0.28208028
[73] 0.40379367 0.37033394 -0.60166487 -0.54092969 -2.25515780 -0.30601571
[79] -0.41863331 -0.57324437 -1.29704473 -0.83641222 1.15809000 -0.21795129
[85] 0.95223121 1.81369230 -0.53749841 -0.95614538 0.53187531 -1.36887333
[91] -0.01900419 1.49081994 0.92274164 1.29143577 0.67171575 -1.48892996
[97] -1.07823643 -0.76084336 -1.07852304 1.08530214
> colSums(tmp)
[1] -1.94945213 0.39189703 1.43780627 -1.39626751 1.06871468 2.82747025
[7] -0.42119140 0.49503923 -0.56440230 -0.17147989 -0.11332199 -0.62873957
[13] -1.12240925 0.85190337 -0.46593677 -0.50190095 -0.68429250 0.18244308
[19] 1.82695041 -0.98754554 -1.27708141 1.10908105 -2.23301063 0.48208871
[25] 1.08557090 1.11424241 -1.14235775 -1.10408440 0.50914517 0.11892653
[31] 1.91689287 -0.94200355 -0.90732974 -0.57611867 -0.14554280 -0.26670855
[37] 0.38202752 0.44268340 2.36244220 -1.10606461 -0.82754724 0.53687027
[43] 0.49085452 2.02500472 -1.74969477 1.07301452 -1.30481524 0.47916396
[49] 1.13579349 0.64956406 -0.72498938 -1.55217473 0.63470977 0.03457418
[55] 1.84255503 1.15279288 1.59471087 0.73980085 0.77321098 -1.59011095
[61] -0.01789707 0.63965088 -1.53225932 0.37377099 0.49848342 -0.02194668
[67] 0.29797176 1.05719650 -1.15344750 0.28478297 -1.12421311 -0.28208028
[73] 0.40379367 0.37033394 -0.60166487 -0.54092969 -2.25515780 -0.30601571
[79] -0.41863331 -0.57324437 -1.29704473 -0.83641222 1.15809000 -0.21795129
[85] 0.95223121 1.81369230 -0.53749841 -0.95614538 0.53187531 -1.36887333
[91] -0.01900419 1.49081994 0.92274164 1.29143577 0.67171575 -1.48892996
[97] -1.07823643 -0.76084336 -1.07852304 1.08530214
> 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] -1.94945213 0.39189703 1.43780627 -1.39626751 1.06871468 2.82747025
[7] -0.42119140 0.49503923 -0.56440230 -0.17147989 -0.11332199 -0.62873957
[13] -1.12240925 0.85190337 -0.46593677 -0.50190095 -0.68429250 0.18244308
[19] 1.82695041 -0.98754554 -1.27708141 1.10908105 -2.23301063 0.48208871
[25] 1.08557090 1.11424241 -1.14235775 -1.10408440 0.50914517 0.11892653
[31] 1.91689287 -0.94200355 -0.90732974 -0.57611867 -0.14554280 -0.26670855
[37] 0.38202752 0.44268340 2.36244220 -1.10606461 -0.82754724 0.53687027
[43] 0.49085452 2.02500472 -1.74969477 1.07301452 -1.30481524 0.47916396
[49] 1.13579349 0.64956406 -0.72498938 -1.55217473 0.63470977 0.03457418
[55] 1.84255503 1.15279288 1.59471087 0.73980085 0.77321098 -1.59011095
[61] -0.01789707 0.63965088 -1.53225932 0.37377099 0.49848342 -0.02194668
[67] 0.29797176 1.05719650 -1.15344750 0.28478297 -1.12421311 -0.28208028
[73] 0.40379367 0.37033394 -0.60166487 -0.54092969 -2.25515780 -0.30601571
[79] -0.41863331 -0.57324437 -1.29704473 -0.83641222 1.15809000 -0.21795129
[85] 0.95223121 1.81369230 -0.53749841 -0.95614538 0.53187531 -1.36887333
[91] -0.01900419 1.49081994 0.92274164 1.29143577 0.67171575 -1.48892996
[97] -1.07823643 -0.76084336 -1.07852304 1.08530214
> colMin(tmp)
[1] -1.94945213 0.39189703 1.43780627 -1.39626751 1.06871468 2.82747025
[7] -0.42119140 0.49503923 -0.56440230 -0.17147989 -0.11332199 -0.62873957
[13] -1.12240925 0.85190337 -0.46593677 -0.50190095 -0.68429250 0.18244308
[19] 1.82695041 -0.98754554 -1.27708141 1.10908105 -2.23301063 0.48208871
[25] 1.08557090 1.11424241 -1.14235775 -1.10408440 0.50914517 0.11892653
[31] 1.91689287 -0.94200355 -0.90732974 -0.57611867 -0.14554280 -0.26670855
[37] 0.38202752 0.44268340 2.36244220 -1.10606461 -0.82754724 0.53687027
[43] 0.49085452 2.02500472 -1.74969477 1.07301452 -1.30481524 0.47916396
[49] 1.13579349 0.64956406 -0.72498938 -1.55217473 0.63470977 0.03457418
[55] 1.84255503 1.15279288 1.59471087 0.73980085 0.77321098 -1.59011095
[61] -0.01789707 0.63965088 -1.53225932 0.37377099 0.49848342 -0.02194668
[67] 0.29797176 1.05719650 -1.15344750 0.28478297 -1.12421311 -0.28208028
[73] 0.40379367 0.37033394 -0.60166487 -0.54092969 -2.25515780 -0.30601571
[79] -0.41863331 -0.57324437 -1.29704473 -0.83641222 1.15809000 -0.21795129
[85] 0.95223121 1.81369230 -0.53749841 -0.95614538 0.53187531 -1.36887333
[91] -0.01900419 1.49081994 0.92274164 1.29143577 0.67171575 -1.48892996
[97] -1.07823643 -0.76084336 -1.07852304 1.08530214
> colMedians(tmp)
[1] -1.94945213 0.39189703 1.43780627 -1.39626751 1.06871468 2.82747025
[7] -0.42119140 0.49503923 -0.56440230 -0.17147989 -0.11332199 -0.62873957
[13] -1.12240925 0.85190337 -0.46593677 -0.50190095 -0.68429250 0.18244308
[19] 1.82695041 -0.98754554 -1.27708141 1.10908105 -2.23301063 0.48208871
[25] 1.08557090 1.11424241 -1.14235775 -1.10408440 0.50914517 0.11892653
[31] 1.91689287 -0.94200355 -0.90732974 -0.57611867 -0.14554280 -0.26670855
[37] 0.38202752 0.44268340 2.36244220 -1.10606461 -0.82754724 0.53687027
[43] 0.49085452 2.02500472 -1.74969477 1.07301452 -1.30481524 0.47916396
[49] 1.13579349 0.64956406 -0.72498938 -1.55217473 0.63470977 0.03457418
[55] 1.84255503 1.15279288 1.59471087 0.73980085 0.77321098 -1.59011095
[61] -0.01789707 0.63965088 -1.53225932 0.37377099 0.49848342 -0.02194668
[67] 0.29797176 1.05719650 -1.15344750 0.28478297 -1.12421311 -0.28208028
[73] 0.40379367 0.37033394 -0.60166487 -0.54092969 -2.25515780 -0.30601571
[79] -0.41863331 -0.57324437 -1.29704473 -0.83641222 1.15809000 -0.21795129
[85] 0.95223121 1.81369230 -0.53749841 -0.95614538 0.53187531 -1.36887333
[91] -0.01900419 1.49081994 0.92274164 1.29143577 0.67171575 -1.48892996
[97] -1.07823643 -0.76084336 -1.07852304 1.08530214
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -1.949452 0.391897 1.437806 -1.396268 1.068715 2.82747 -0.4211914
[2,] -1.949452 0.391897 1.437806 -1.396268 1.068715 2.82747 -0.4211914
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.4950392 -0.5644023 -0.1714799 -0.113322 -0.6287396 -1.122409 0.8519034
[2,] 0.4950392 -0.5644023 -0.1714799 -0.113322 -0.6287396 -1.122409 0.8519034
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -0.4659368 -0.5019009 -0.6842925 0.1824431 1.82695 -0.9875455 -1.277081
[2,] -0.4659368 -0.5019009 -0.6842925 0.1824431 1.82695 -0.9875455 -1.277081
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 1.109081 -2.233011 0.4820887 1.085571 1.114242 -1.142358 -1.104084
[2,] 1.109081 -2.233011 0.4820887 1.085571 1.114242 -1.142358 -1.104084
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.5091452 0.1189265 1.916893 -0.9420036 -0.9073297 -0.5761187 -0.1455428
[2,] 0.5091452 0.1189265 1.916893 -0.9420036 -0.9073297 -0.5761187 -0.1455428
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -0.2667085 0.3820275 0.4426834 2.362442 -1.106065 -0.8275472 0.5368703
[2,] -0.2667085 0.3820275 0.4426834 2.362442 -1.106065 -0.8275472 0.5368703
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.4908545 2.025005 -1.749695 1.073015 -1.304815 0.479164 1.135793
[2,] 0.4908545 2.025005 -1.749695 1.073015 -1.304815 0.479164 1.135793
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.6495641 -0.7249894 -1.552175 0.6347098 0.03457418 1.842555 1.152793
[2,] 0.6495641 -0.7249894 -1.552175 0.6347098 0.03457418 1.842555 1.152793
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 1.594711 0.7398008 0.773211 -1.590111 -0.01789707 0.6396509 -1.532259
[2,] 1.594711 0.7398008 0.773211 -1.590111 -0.01789707 0.6396509 -1.532259
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.373771 0.4984834 -0.02194668 0.2979718 1.057197 -1.153447 0.284783
[2,] 0.373771 0.4984834 -0.02194668 0.2979718 1.057197 -1.153447 0.284783
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -1.124213 -0.2820803 0.4037937 0.3703339 -0.6016649 -0.5409297 -2.255158
[2,] -1.124213 -0.2820803 0.4037937 0.3703339 -0.6016649 -0.5409297 -2.255158
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -0.3060157 -0.4186333 -0.5732444 -1.297045 -0.8364122 1.15809 -0.2179513
[2,] -0.3060157 -0.4186333 -0.5732444 -1.297045 -0.8364122 1.15809 -0.2179513
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 0.9522312 1.813692 -0.5374984 -0.9561454 0.5318753 -1.368873 -0.01900419
[2,] 0.9522312 1.813692 -0.5374984 -0.9561454 0.5318753 -1.368873 -0.01900419
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 1.49082 0.9227416 1.291436 0.6717157 -1.48893 -1.078236 -0.7608434
[2,] 1.49082 0.9227416 1.291436 0.6717157 -1.48893 -1.078236 -0.7608434
[,99] [,100]
[1,] -1.078523 1.085302
[2,] -1.078523 1.085302
>
>
> Max(tmp2)
[1] 2.873335
> Min(tmp2)
[1] -2.673227
> mean(tmp2)
[1] 0.02648764
> Sum(tmp2)
[1] 2.648764
> Var(tmp2)
[1] 1.107718
>
> rowMeans(tmp2)
[1] -0.48778733 -1.07059943 -1.46187613 0.99855418 0.75626820 0.64827292
[7] -2.67322728 -0.49003942 -0.72781691 0.56081168 1.72618049 0.70257503
[13] -0.09329040 -0.20119651 0.31081632 0.92318112 -1.08141669 1.42753090
[19] 0.46632796 -0.06844092 1.04970722 0.01221888 0.08854149 -1.26209900
[25] -0.59015581 0.52485441 -0.44015257 1.51268811 -0.02933179 0.47137754
[31] -0.18156410 0.11285693 0.51953953 -0.47242805 -0.96632758 -0.38263215
[37] 1.01117296 1.44661354 0.10600716 -0.53779466 -1.84242899 -1.45544390
[43] 0.71553891 0.43792743 -1.60047690 -0.67176954 0.07128058 -0.45788257
[49] -1.38010875 0.12472266 1.82857972 -1.74835855 -0.42060888 -0.90533210
[55] 1.88743192 -0.00382344 0.99583742 0.21862174 1.31057055 0.82968167
[61] -1.28209200 0.25894345 0.80491703 1.57132306 1.48127989 1.24538955
[67] -0.19107665 -1.50021512 -0.47228148 -1.80553361 -0.87125295 2.87333497
[73] 0.74417099 -0.32427505 0.39596796 -0.92525444 0.85196571 0.87483847
[79] 0.16630607 -1.35918740 0.19284782 1.02834502 -0.50438516 2.07445112
[85] -1.01612545 -0.18450088 -1.61525510 -0.48896284 -0.88343661 -1.01320283
[91] 1.46283816 0.49680562 -0.41104045 1.19139230 -0.08508945 0.89890064
[97] -0.58588873 -1.77980703 -0.47780521 1.71953621
> rowSums(tmp2)
[1] -0.48778733 -1.07059943 -1.46187613 0.99855418 0.75626820 0.64827292
[7] -2.67322728 -0.49003942 -0.72781691 0.56081168 1.72618049 0.70257503
[13] -0.09329040 -0.20119651 0.31081632 0.92318112 -1.08141669 1.42753090
[19] 0.46632796 -0.06844092 1.04970722 0.01221888 0.08854149 -1.26209900
[25] -0.59015581 0.52485441 -0.44015257 1.51268811 -0.02933179 0.47137754
[31] -0.18156410 0.11285693 0.51953953 -0.47242805 -0.96632758 -0.38263215
[37] 1.01117296 1.44661354 0.10600716 -0.53779466 -1.84242899 -1.45544390
[43] 0.71553891 0.43792743 -1.60047690 -0.67176954 0.07128058 -0.45788257
[49] -1.38010875 0.12472266 1.82857972 -1.74835855 -0.42060888 -0.90533210
[55] 1.88743192 -0.00382344 0.99583742 0.21862174 1.31057055 0.82968167
[61] -1.28209200 0.25894345 0.80491703 1.57132306 1.48127989 1.24538955
[67] -0.19107665 -1.50021512 -0.47228148 -1.80553361 -0.87125295 2.87333497
[73] 0.74417099 -0.32427505 0.39596796 -0.92525444 0.85196571 0.87483847
[79] 0.16630607 -1.35918740 0.19284782 1.02834502 -0.50438516 2.07445112
[85] -1.01612545 -0.18450088 -1.61525510 -0.48896284 -0.88343661 -1.01320283
[91] 1.46283816 0.49680562 -0.41104045 1.19139230 -0.08508945 0.89890064
[97] -0.58588873 -1.77980703 -0.47780521 1.71953621
> 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] -0.48778733 -1.07059943 -1.46187613 0.99855418 0.75626820 0.64827292
[7] -2.67322728 -0.49003942 -0.72781691 0.56081168 1.72618049 0.70257503
[13] -0.09329040 -0.20119651 0.31081632 0.92318112 -1.08141669 1.42753090
[19] 0.46632796 -0.06844092 1.04970722 0.01221888 0.08854149 -1.26209900
[25] -0.59015581 0.52485441 -0.44015257 1.51268811 -0.02933179 0.47137754
[31] -0.18156410 0.11285693 0.51953953 -0.47242805 -0.96632758 -0.38263215
[37] 1.01117296 1.44661354 0.10600716 -0.53779466 -1.84242899 -1.45544390
[43] 0.71553891 0.43792743 -1.60047690 -0.67176954 0.07128058 -0.45788257
[49] -1.38010875 0.12472266 1.82857972 -1.74835855 -0.42060888 -0.90533210
[55] 1.88743192 -0.00382344 0.99583742 0.21862174 1.31057055 0.82968167
[61] -1.28209200 0.25894345 0.80491703 1.57132306 1.48127989 1.24538955
[67] -0.19107665 -1.50021512 -0.47228148 -1.80553361 -0.87125295 2.87333497
[73] 0.74417099 -0.32427505 0.39596796 -0.92525444 0.85196571 0.87483847
[79] 0.16630607 -1.35918740 0.19284782 1.02834502 -0.50438516 2.07445112
[85] -1.01612545 -0.18450088 -1.61525510 -0.48896284 -0.88343661 -1.01320283
[91] 1.46283816 0.49680562 -0.41104045 1.19139230 -0.08508945 0.89890064
[97] -0.58588873 -1.77980703 -0.47780521 1.71953621
> rowMin(tmp2)
[1] -0.48778733 -1.07059943 -1.46187613 0.99855418 0.75626820 0.64827292
[7] -2.67322728 -0.49003942 -0.72781691 0.56081168 1.72618049 0.70257503
[13] -0.09329040 -0.20119651 0.31081632 0.92318112 -1.08141669 1.42753090
[19] 0.46632796 -0.06844092 1.04970722 0.01221888 0.08854149 -1.26209900
[25] -0.59015581 0.52485441 -0.44015257 1.51268811 -0.02933179 0.47137754
[31] -0.18156410 0.11285693 0.51953953 -0.47242805 -0.96632758 -0.38263215
[37] 1.01117296 1.44661354 0.10600716 -0.53779466 -1.84242899 -1.45544390
[43] 0.71553891 0.43792743 -1.60047690 -0.67176954 0.07128058 -0.45788257
[49] -1.38010875 0.12472266 1.82857972 -1.74835855 -0.42060888 -0.90533210
[55] 1.88743192 -0.00382344 0.99583742 0.21862174 1.31057055 0.82968167
[61] -1.28209200 0.25894345 0.80491703 1.57132306 1.48127989 1.24538955
[67] -0.19107665 -1.50021512 -0.47228148 -1.80553361 -0.87125295 2.87333497
[73] 0.74417099 -0.32427505 0.39596796 -0.92525444 0.85196571 0.87483847
[79] 0.16630607 -1.35918740 0.19284782 1.02834502 -0.50438516 2.07445112
[85] -1.01612545 -0.18450088 -1.61525510 -0.48896284 -0.88343661 -1.01320283
[91] 1.46283816 0.49680562 -0.41104045 1.19139230 -0.08508945 0.89890064
[97] -0.58588873 -1.77980703 -0.47780521 1.71953621
>
> colMeans(tmp2)
[1] 0.02648764
> colSums(tmp2)
[1] 2.648764
> colVars(tmp2)
[1] 1.107718
> colSd(tmp2)
[1] 1.052482
> colMax(tmp2)
[1] 2.873335
> colMin(tmp2)
[1] -2.673227
> colMedians(tmp2)
[1] 0.004197721
> colRanges(tmp2)
[,1]
[1,] -2.673227
[2,] 2.873335
>
> 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] 2.0599348 1.5000061 -3.0529192 1.7831581 1.5827076 -2.0601493
[7] -2.4301214 -0.6395158 -2.4118026 -2.3505189
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.8797482
[2,] -0.7590189
[3,] 0.2861200
[4,] 0.9489606
[5,] 2.9936920
>
> rowApply(tmp,sum)
[1] -4.2717088 -1.8248483 1.2291287 -2.3140896 -1.7416583 -1.5849911
[7] 0.9236107 1.1456920 -0.3057775 2.7254216
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 10 6 10 3 8 3 6 2 10
[2,] 10 6 5 7 7 10 1 8 5 6
[3,] 6 4 7 1 2 3 4 7 8 5
[4,] 4 1 8 6 8 9 10 10 6 2
[5,] 9 7 1 5 6 5 6 3 9 9
[6,] 5 3 4 8 1 7 2 9 7 4
[7,] 7 5 10 4 4 4 5 4 4 1
[8,] 3 2 3 9 10 6 8 1 10 7
[9,] 8 9 2 2 5 1 9 2 3 8
[10,] 2 8 9 3 9 2 7 5 1 3
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 2.3056614 -2.2970784 0.4121411 -0.7385228 2.2703971 -0.3338151
[7] -2.0245229 1.0942885 -0.4173805 3.3339587 4.1849694 0.3201329
[13] 0.2223674 -2.4772706 -1.9090436 2.7180831 -4.6801567 3.7710313
[19] 0.8975202 -0.9590502
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.4914683
[2,] 0.2051142
[3,] 0.4337570
[4,] 0.5728652
[5,] 1.5853932
>
> rowApply(tmp,sum)
[1] 5.932974 -2.461393 -4.034372 -2.042500 8.299002
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 13 7 16 19 7
[2,] 5 15 7 15 1
[3,] 6 12 12 18 6
[4,] 20 13 1 3 14
[5,] 10 10 13 13 19
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.5728652 -0.5368757 -0.46821280 1.7656009 0.16464174 -0.8911637
[2,] -0.4914683 0.2911762 0.01250859 0.1544560 -0.20527365 1.0624735
[3,] 0.4337570 -0.6019905 0.06174264 -1.8165356 0.06716027 -0.3528946
[4,] 1.5853932 0.6311371 0.82629706 -1.6306857 0.33927642 -0.5033809
[5,] 0.2051142 -2.0805256 -0.02019437 0.7886416 1.90459235 0.3511506
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 1.2755369 1.4156051 -0.14039519 1.6091240 0.882231 1.25776607
[2,] -0.8735744 1.1358432 -0.88742446 0.8800240 -1.644250 -0.72381678
[3,] -0.0891465 -0.8852116 0.25638065 -1.2599980 1.234365 -0.58440664
[4,] -1.0924616 0.5528552 -0.05372724 0.6388917 2.007771 0.08478652
[5,] -1.2448773 -1.1248034 0.40778578 1.4659170 1.704853 0.28580369
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.5294543 -0.7159784 -1.5879436 0.6348232 -0.5415037 0.4103649
[2,] 1.2010132 -1.2269641 -0.4241270 -0.3440021 -1.6045513 1.1844516
[3,] -1.6099601 -0.1719363 -0.8197638 1.0628990 -1.0081270 0.3695489
[4,] -0.3152101 -0.8949010 -0.5819239 -1.6761206 -1.7671016 0.7946594
[5,] 0.4170701 0.5325093 1.5047146 3.0404835 0.2411268 1.0120065
[,19] [,20]
[1,] 0.1479276 0.1491060
[2,] -0.1770910 0.2192045
[3,] 0.9207930 0.7589522
[4,] 0.3099817 -1.2980366
[5,] -0.3040911 -0.7882764
>
>
> 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 : 649 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 : 561 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 0.8312135 -0.07068187 0.6755393 0.1590313 1.351373 0.8828289 -0.6926102
col8 col9 col10 col11 col12 col13 col14
row1 -1.999212 -0.1782008 -0.1813827 0.2094689 0.2403724 -0.6980598 -0.4759757
col15 col16 col17 col18 col19 col20
row1 -1.017623 -1.288185 -1.672947 0.1911784 -0.532479 1.124954
> tmp[,"col10"]
col10
row1 -0.18138269
row2 0.07319198
row3 0.61328315
row4 0.88599034
row5 -0.37880066
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 0.8312135 -0.07068187 0.6755393 0.1590313 1.351373 0.8828289 -0.6926102
row5 -0.3562806 -0.19814684 0.4814312 -0.2724620 1.180771 -0.8744125 0.8259779
col8 col9 col10 col11 col12 col13
row1 -1.9992125 -0.1782008 -0.1813827 0.2094689 0.2403724 -0.6980598
row5 0.6051086 0.9219119 -0.3788007 -0.8803247 -0.5955106 0.6871898
col14 col15 col16 col17 col18 col19
row1 -0.4759757 -1.0176233 -1.288185 -1.67294696 0.1911784 -0.5324790
row5 -0.4907195 0.7180016 -1.529672 -0.05645163 0.9390966 -0.5791561
col20
row1 1.1249535
row5 -0.8726197
> tmp[,c("col6","col20")]
col6 col20
row1 0.8828289 1.1249535
row2 -1.2311543 -0.4335212
row3 2.6317581 -0.4424526
row4 -1.1126207 0.5375096
row5 -0.8744125 -0.8726197
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.8828289 1.1249535
row5 -0.8744125 -0.8726197
>
>
>
>
> 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 51.00215 48.59817 50.44004 52.38356 50.34235 103.3047 48.4664 50.61115
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.64164 47.40382 49.75011 49.70037 49.66066 49.07567 50.30263 51.39337
col17 col18 col19 col20
row1 49.88699 48.7362 48.98531 106.7634
> tmp[,"col10"]
col10
row1 47.40382
row2 29.06104
row3 30.66389
row4 29.68919
row5 50.24670
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 51.00215 48.59817 50.44004 52.38356 50.34235 103.3047 48.46640 50.61115
row5 50.61569 50.65240 49.99100 50.21722 51.10328 103.6416 48.45517 51.03277
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.64164 47.40382 49.75011 49.70037 49.66066 49.07567 50.30263 51.39337
row5 49.03946 50.24670 49.83387 48.69681 50.85654 49.59817 50.44922 50.37607
col17 col18 col19 col20
row1 49.88699 48.73620 48.98531 106.7634
row5 51.17218 48.90495 49.12192 106.2432
> tmp[,c("col6","col20")]
col6 col20
row1 103.30468 106.76335
row2 73.54356 77.80416
row3 74.12910 75.13502
row4 76.09612 73.53386
row5 103.64159 106.24322
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 103.3047 106.7634
row5 103.6416 106.2432
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 103.3047 106.7634
row5 103.6416 106.2432
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 1.1892939
[2,] 0.5545592
[3,] 1.4421278
[4,] 1.8285989
[5,] 0.9561708
> tmp[,c("col17","col7")]
col17 col7
[1,] 0.4696735 0.5749698
[2,] -0.1622457 1.2090365
[3,] 0.6977663 -1.4754588
[4,] 1.5855189 1.1353875
[5,] -1.0117198 -0.1407486
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.7908005 0.7356725
[2,] 1.7079232 1.0557264
[3,] -0.2663416 -0.9649334
[4,] 1.0570027 1.5387384
[5,] -1.7295355 -0.0344728
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.7908005
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.7908005
[2,] 1.7079232
>
>
>
> 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 -0.8270696 0.3657214 -0.1091410 1.0233053 0.2931130 0.04841397
row1 0.4682141 -0.5320078 0.8482256 -0.7921137 -0.6695953 -1.12537018
[,7] [,8] [,9] [,10] [,11] [,12] [,13]
row3 -1.114009 -1.9195844 0.1577085 -0.2454850 0.7086237 -0.2872479 1.0407163
row1 0.448327 0.8519202 0.5124673 -0.6823471 -0.2239177 0.8365691 0.2917202
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 0.6622571 3.021412 0.31641522 0.2024441 0.07426058 1.11448603 1.0108481
row1 0.2193202 -1.878897 0.06842748 1.0533282 0.91098783 0.09892874 -0.3379332
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.7244148 0.549797 0.8882308 -0.1563576 -1.306235 0.3485954 2.346983
[,8] [,9] [,10]
row2 -0.5518763 -0.7486733 0.3114526
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -0.3662374 -1.500959 -1.350679 -0.8912966 1.084677 0.1486823 -0.8886288
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -1.207939 0.7950598 0.871042 0.4108884 0.6531807 -0.5394376 0.2212647
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.516201 -0.04988961 0.760881 -1.296944 0.995656 1.351576
>
>
> 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: 0x55ccc7682060>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMbcf3e7ae29030"
[2] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMbcf3e542650d3"
[3] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMbcf3e1d166e0e"
[4] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMbcf3e7c3c6c61"
[5] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMbcf3e5da02"
[6] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMbcf3e504ae04f"
[7] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMbcf3e6188fc22"
[8] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMbcf3e1067f8a6"
[9] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMbcf3e10300943"
[10] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMbcf3e485171a1"
[11] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMbcf3e68025e71"
[12] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMbcf3e7842e579"
[13] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMbcf3e589201"
[14] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMbcf3e4407dd41"
[15] "/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMbcf3e60e41f4b"
>
>
> ### 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: 0x55ccc7dad6f0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x55ccc7dad6f0>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x55ccc7dad6f0>
> rowMedians(tmp)
[1] 0.51456060 0.55328824 0.43694586 -0.05860133 -0.22900526 -0.18399516
[7] -0.10690837 0.14189496 0.32063310 -0.06201356 0.11139092 0.02441274
[13] -0.70868484 0.13481658 0.13028588 0.21833049 -0.14742724 0.05330837
[19] -0.22161310 0.30038449 -0.73291125 -0.01034324 0.40506447 0.17341935
[25] -0.09601898 0.18551876 0.02912421 0.10571620 -0.37956880 0.38841439
[31] -0.39112164 0.19909390 -0.17021091 0.12540505 0.30947660 -0.08981412
[37] -0.03612705 -0.49427307 -0.67097450 -0.03891503 0.21680232 0.13135004
[43] 0.20612374 0.34754656 0.40338952 0.52567048 -0.32258657 0.05511528
[49] 0.13182001 -0.71309075 -0.03384432 0.24526421 0.33427372 -0.34371359
[55] -0.04400573 0.30148040 -0.02243392 0.16324873 0.18045321 -0.13885310
[61] -0.29423173 -0.21626298 0.31586647 0.20735421 -0.08743854 -0.02693569
[67] 0.18101307 0.32635224 -0.46760597 0.20722083 0.02482587 0.80478517
[73] 0.06659961 0.32899597 0.01372791 0.06740623 -0.24106777 0.59208497
[79] 0.47749901 -0.02401340 0.04374445 0.60586878 0.14437191 0.35586522
[85] 0.49865286 0.10144478 0.46416154 -0.17238568 -0.54322408 -0.24592388
[91] -0.07878857 -0.77213729 -0.23636377 -0.50479602 0.75874308 -0.28544363
[97] 0.34041449 0.12281895 -0.29604203 0.26716243 -0.22781487 0.20099156
[103] -0.83052526 0.10746092 0.27311974 0.55640621 -0.61174512 -0.28905624
[109] -0.33436350 -0.29768437 0.13931253 0.12845283 0.36558102 -0.17061436
[115] 0.06870926 0.09405734 0.10285456 -0.43551482 -0.17698373 0.41109776
[121] 0.12590321 -0.46211825 -0.20016587 0.07913554 0.24330983 0.03316553
[127] -0.45375672 0.47479849 0.72609881 -0.01968566 0.77414681 0.05486442
[133] -0.38610940 -0.20620451 -0.05917728 -0.43105216 -0.19033078 0.21590704
[139] -0.33349000 -0.03390713 -0.11666089 0.01992092 0.63727345 -0.08626713
[145] -0.13590698 0.22451454 -0.07894727 0.08365073 -0.46138854 0.35428889
[151] 0.29240797 -0.04635330 -0.49084455 -0.20376182 -0.01393536 -0.78326614
[157] -0.07812564 -0.50550524 -0.24819015 0.19973431 0.05446264 0.10106078
[163] 0.41379172 -0.10443815 -0.07313573 -0.18688564 0.04845054 -0.50066695
[169] -0.30223973 0.34454341 0.19937416 0.38340272 0.41597181 -0.19116424
[175] 0.64291449 -0.02167023 -0.28044670 -0.14044366 0.25996991 -0.42962792
[181] -0.20468677 -0.16246186 -0.15975485 0.36444249 -0.04125946 -0.06699975
[187] 0.56335825 -0.06246400 0.16731531 0.01875570 -0.24708560 -0.46907952
[193] 0.15732379 0.13330620 0.43660924 -0.37982546 -0.92200643 -0.09762303
[199] -0.29122325 -0.26915655 0.19396497 -0.11391654 -0.05411825 -0.30133097
[205] 0.02579954 -0.30726001 0.14563834 -0.26863188 -0.31084271 0.69163190
[211] 0.29030528 0.52527581 0.35251798 0.38822179 0.46191653 0.32943058
[217] 0.38027237 0.05040715 0.57342753 -0.13031360 -0.43081511 0.17161348
[223] -0.14223724 -0.51184088 -0.42325922 -0.30642342 -0.13412669 0.26835493
[229] 0.05115640 -0.12537024
>
> proc.time()
user system elapsed
1.241 0.673 1.910
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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: 0x55e694308950>
> .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: 0x55e694308950>
> .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: 0x55e694308950>
> .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: 0x55e694308950>
> 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: 0x55e695b88860>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55e695b88860>
> .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: 0x55e695b88860>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55e695b88860>
> .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: 0x55e695b88860>
> 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: 0x55e695bd3c10>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55e695bd3c10>
> .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: 0x55e695bd3c10>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x55e695bd3c10>
> .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: 0x55e695bd3c10>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x55e695bd3c10>
> .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: 0x55e695bd3c10>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x55e695bd3c10>
> .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: 0x55e695bd3c10>
> 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: 0x55e695571230>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x55e695571230>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55e695571230>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55e695571230>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFilebd0cc3544a1a1" "BufferedMatrixFilebd0cc36e87a04"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFilebd0cc3544a1a1" "BufferedMatrixFilebd0cc36e87a04"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x55e694889700>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55e694889700>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x55e694889700>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x55e694889700>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x55e694889700>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x55e694889700>
> .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: 0x55e6948c9050>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55e6948c9050>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x55e6948c9050>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x55e6948c9050>
> 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: 0x55e694a4aa30>
> .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: 0x55e694a4aa30>
> rm(P)
>
> proc.time()
user system elapsed
0.276 0.045 0.310
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
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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
0.263 0.041 0.290