Ben Bolstad
| Snapshot Date: 2026-02-09 13:45 -0500 (Mon, 09 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: RELEASE_3_22 |
| git_last_commit: d2ce144 |
| git_last_commit_date: 2025-10-29 09:58:55 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-12 11:58 -0500 (Thu, 12 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4889 |
| 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 257/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.74.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for BufferedMatrix in R Universe. | ||||||||||||||
|
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: 1.74.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BufferedMatrix_1.74.0.tar.gz |
| StartedAt: 2026-02-09 22:07:03 -0500 (Mon, 09 Feb 2026) |
| EndedAt: 2026-02-09 22:07:27 -0500 (Mon, 09 Feb 2026) |
| EllapsedTime: 24.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BufferedMatrix_1.74.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.74.0’
* 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 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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-3.22-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.74.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function ‘dbm_ReadOnlyMode’:
doubleBufferedMatrix.c:1580:7: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
1580 | if (!(Matrix->readonly) & setting){
| ^~~~~~~~~~~~~~~~~~~
doubleBufferedMatrix.c: At top level:
doubleBufferedMatrix.c:3327:12: warning: ‘sort_double’ defined but not used [-Wunused-function]
3327 | static int sort_double(const double *a1,const double *a2){
| ^~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c init_package.c -o init_package.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-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-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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
0.230 0.048 0.267
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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-3.22-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 478284 25.6 1046725 56 639600 34.2
Vcells 884773 6.8 8388608 64 2081613 15.9
>
>
>
>
> ##
> ## 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] "Mon Feb 9 22:07:18 2026"
> 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] "Mon Feb 9 22:07:18 2026"
>
>
> 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: 0x58434008d370>
>
>
>
> 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] "Mon Feb 9 22:07:18 2026"
> 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] "Mon Feb 9 22:07:19 2026"
>
> ColMode(tmp2)
<pointer: 0x58434008d370>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.4384605 0.7120208 -0.4235084 -3.5061695
[2,] -0.4989300 0.1038517 0.7159239 -0.9533981
[3,] 0.1634588 -1.0819235 -0.1106358 -1.5311680
[4,] -1.1738366 -0.8329678 0.2049847 0.1970734
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-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,] 99.4384605 0.7120208 0.4235084 3.5061695
[2,] 0.4989300 0.1038517 0.7159239 0.9533981
[3,] 0.1634588 1.0819235 0.1106358 1.5311680
[4,] 1.1738366 0.8329678 0.2049847 0.1970734
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-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,] 9.9718835 0.8438133 0.6507752 1.8724768
[2,] 0.7063497 0.3222603 0.8461229 0.9764211
[3,] 0.4043004 1.0401555 0.3326196 1.2374037
[4,] 1.0834374 0.9126707 0.4527524 0.4439295
>
> 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-3.22-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,] 224.15730 34.15015 31.93126 47.23094
[2,] 32.56243 28.32645 34.17715 35.71761
[3,] 29.20646 36.48348 28.43683 38.90521
[4,] 37.00821 34.95967 29.73251 29.63637
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x5843410899b0>
> exp(tmp5)
<pointer: 0x5843410899b0>
> log(tmp5,2)
<pointer: 0x5843410899b0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 466.554
> Min(tmp5)
[1] 52.88341
> mean(tmp5)
[1] 73.11951
> Sum(tmp5)
[1] 14623.9
> Var(tmp5)
[1] 871.0126
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 92.21562 66.21794 71.43398 72.60867 72.90307 68.76114 70.79593 75.74221
[9] 69.38402 71.13251
> rowSums(tmp5)
[1] 1844.312 1324.359 1428.680 1452.173 1458.061 1375.223 1415.919 1514.844
[9] 1387.680 1422.650
> rowVars(tmp5)
[1] 7839.94600 85.63015 115.80184 83.23456 106.07435 53.80968
[7] 102.17905 105.26496 65.43062 76.26943
> rowSd(tmp5)
[1] 88.543470 9.253656 10.761126 9.123298 10.299240 7.335508 10.108365
[8] 10.259871 8.088919 8.733237
> rowMax(tmp5)
[1] 466.55404 88.23968 93.36382 90.61234 92.67311 80.99836 95.36788
[8] 100.09100 88.83596 85.64991
> rowMin(tmp5)
[1] 60.57055 54.51876 54.92899 58.73409 55.60542 55.52615 57.72495 60.45803
[9] 55.47404 52.88341
>
> colMeans(tmp5)
[1] 108.37504 68.70378 70.44293 70.41547 68.95939 72.82981 74.89901
[8] 75.24254 72.08798 73.67998 65.70852 68.17631 67.46976 70.69195
[15] 75.04057 72.46039 68.75761 72.67025 71.25984 74.51909
> colSums(tmp5)
[1] 1083.7504 687.0378 704.4293 704.1547 689.5939 728.2981 748.9901
[8] 752.4254 720.8798 736.7998 657.0852 681.7631 674.6976 706.9195
[15] 750.4057 724.6039 687.5761 726.7025 712.5984 745.1909
> colVars(tmp5)
[1] 15914.90947 65.59549 68.39414 154.56980 75.30117 59.00006
[7] 149.53380 103.35324 73.29813 141.16994 67.85069 111.00095
[13] 74.72290 85.06460 37.47888 86.95970 84.08785 33.41538
[19] 82.91739 180.08842
> colSd(tmp5)
[1] 126.154308 8.099104 8.270075 12.432610 8.677625 7.681150
[7] 12.228401 10.166280 8.561433 11.881496 8.237153 10.535699
[13] 8.644241 9.223047 6.122000 9.325219 9.169943 5.780604
[19] 9.105899 13.419703
> colMax(tmp5)
[1] 466.55404 84.82195 85.64991 98.30501 82.48884 85.90660 90.61234
[8] 95.36788 86.05449 92.67311 81.11356 86.32731 86.86380 88.23968
[15] 84.41897 87.11508 88.83596 81.49968 93.36382 100.09100
> colMin(tmp5)
[1] 55.47404 58.95780 59.18754 52.88341 57.78301 63.27835 58.28222 55.56668
[9] 56.63364 54.51876 54.92899 55.60542 55.52615 56.71332 64.54693 59.73173
[17] 58.73409 63.21470 63.02185 55.80735
>
>
> ### 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] 92.21562 NA 71.43398 72.60867 72.90307 68.76114 70.79593 75.74221
[9] 69.38402 71.13251
> rowSums(tmp5)
[1] 1844.312 NA 1428.680 1452.173 1458.061 1375.223 1415.919 1514.844
[9] 1387.680 1422.650
> rowVars(tmp5)
[1] 7839.94600 82.38323 115.80184 83.23456 106.07435 53.80968
[7] 102.17905 105.26496 65.43062 76.26943
> rowSd(tmp5)
[1] 88.543470 9.076521 10.761126 9.123298 10.299240 7.335508 10.108365
[8] 10.259871 8.088919 8.733237
> rowMax(tmp5)
[1] 466.55404 NA 93.36382 90.61234 92.67311 80.99836 95.36788
[8] 100.09100 88.83596 85.64991
> rowMin(tmp5)
[1] 60.57055 NA 54.92899 58.73409 55.60542 55.52615 57.72495 60.45803
[9] 55.47404 52.88341
>
> colMeans(tmp5)
[1] 108.37504 68.70378 70.44293 70.41547 68.95939 72.82981 74.89901
[8] 75.24254 72.08798 NA 65.70852 68.17631 67.46976 70.69195
[15] 75.04057 72.46039 68.75761 72.67025 71.25984 74.51909
> colSums(tmp5)
[1] 1083.7504 687.0378 704.4293 704.1547 689.5939 728.2981 748.9901
[8] 752.4254 720.8798 NA 657.0852 681.7631 674.6976 706.9195
[15] 750.4057 724.6039 687.5761 726.7025 712.5984 745.1909
> colVars(tmp5)
[1] 15914.90947 65.59549 68.39414 154.56980 75.30117 59.00006
[7] 149.53380 103.35324 73.29813 NA 67.85069 111.00095
[13] 74.72290 85.06460 37.47888 86.95970 84.08785 33.41538
[19] 82.91739 180.08842
> colSd(tmp5)
[1] 126.154308 8.099104 8.270075 12.432610 8.677625 7.681150
[7] 12.228401 10.166280 8.561433 NA 8.237153 10.535699
[13] 8.644241 9.223047 6.122000 9.325219 9.169943 5.780604
[19] 9.105899 13.419703
> colMax(tmp5)
[1] 466.55404 84.82195 85.64991 98.30501 82.48884 85.90660 90.61234
[8] 95.36788 86.05449 NA 81.11356 86.32731 86.86380 88.23968
[15] 84.41897 87.11508 88.83596 81.49968 93.36382 100.09100
> colMin(tmp5)
[1] 55.47404 58.95780 59.18754 52.88341 57.78301 63.27835 58.28222 55.56668
[9] 56.63364 NA 54.92899 55.60542 55.52615 56.71332 64.54693 59.73173
[17] 58.73409 63.21470 63.02185 55.80735
>
> Max(tmp5,na.rm=TRUE)
[1] 466.554
> Min(tmp5,na.rm=TRUE)
[1] 52.88341
> mean(tmp5,na.rm=TRUE)
[1] 73.21298
> Sum(tmp5,na.rm=TRUE)
[1] 14569.38
> Var(tmp5,na.rm=TRUE)
[1] 873.6555
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.21562 66.83369 71.43398 72.60867 72.90307 68.76114 70.79593 75.74221
[9] 69.38402 71.13251
> rowSums(tmp5,na.rm=TRUE)
[1] 1844.312 1269.840 1428.680 1452.173 1458.061 1375.223 1415.919 1514.844
[9] 1387.680 1422.650
> rowVars(tmp5,na.rm=TRUE)
[1] 7839.94600 82.38323 115.80184 83.23456 106.07435 53.80968
[7] 102.17905 105.26496 65.43062 76.26943
> rowSd(tmp5,na.rm=TRUE)
[1] 88.543470 9.076521 10.761126 9.123298 10.299240 7.335508 10.108365
[8] 10.259871 8.088919 8.733237
> rowMax(tmp5,na.rm=TRUE)
[1] 466.55404 88.23968 93.36382 90.61234 92.67311 80.99836 95.36788
[8] 100.09100 88.83596 85.64991
> rowMin(tmp5,na.rm=TRUE)
[1] 60.57055 55.80735 54.92899 58.73409 55.60542 55.52615 57.72495 60.45803
[9] 55.47404 52.88341
>
> colMeans(tmp5,na.rm=TRUE)
[1] 108.37504 68.70378 70.44293 70.41547 68.95939 72.82981 74.89901
[8] 75.24254 72.08798 75.80901 65.70852 68.17631 67.46976 70.69195
[15] 75.04057 72.46039 68.75761 72.67025 71.25984 74.51909
> colSums(tmp5,na.rm=TRUE)
[1] 1083.7504 687.0378 704.4293 704.1547 689.5939 728.2981 748.9901
[8] 752.4254 720.8798 682.2811 657.0852 681.7631 674.6976 706.9195
[15] 750.4057 724.6039 687.5761 726.7025 712.5984 745.1909
> colVars(tmp5,na.rm=TRUE)
[1] 15914.90947 65.59549 68.39414 154.56980 75.30117 59.00006
[7] 149.53380 103.35324 73.29813 107.82275 67.85069 111.00095
[13] 74.72290 85.06460 37.47888 86.95970 84.08785 33.41538
[19] 82.91739 180.08842
> colSd(tmp5,na.rm=TRUE)
[1] 126.154308 8.099104 8.270075 12.432610 8.677625 7.681150
[7] 12.228401 10.166280 8.561433 10.383773 8.237153 10.535699
[13] 8.644241 9.223047 6.122000 9.325219 9.169943 5.780604
[19] 9.105899 13.419703
> colMax(tmp5,na.rm=TRUE)
[1] 466.55404 84.82195 85.64991 98.30501 82.48884 85.90660 90.61234
[8] 95.36788 86.05449 92.67311 81.11356 86.32731 86.86380 88.23968
[15] 84.41897 87.11508 88.83596 81.49968 93.36382 100.09100
> colMin(tmp5,na.rm=TRUE)
[1] 55.47404 58.95780 59.18754 52.88341 57.78301 63.27835 58.28222 55.56668
[9] 56.63364 62.81564 54.92899 55.60542 55.52615 56.71332 64.54693 59.73173
[17] 58.73409 63.21470 63.02185 55.80735
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.21562 NaN 71.43398 72.60867 72.90307 68.76114 70.79593 75.74221
[9] 69.38402 71.13251
> rowSums(tmp5,na.rm=TRUE)
[1] 1844.312 0.000 1428.680 1452.173 1458.061 1375.223 1415.919 1514.844
[9] 1387.680 1422.650
> rowVars(tmp5,na.rm=TRUE)
[1] 7839.94600 NA 115.80184 83.23456 106.07435 53.80968
[7] 102.17905 105.26496 65.43062 76.26943
> rowSd(tmp5,na.rm=TRUE)
[1] 88.543470 NA 10.761126 9.123298 10.299240 7.335508 10.108365
[8] 10.259871 8.088919 8.733237
> rowMax(tmp5,na.rm=TRUE)
[1] 466.55404 NA 93.36382 90.61234 92.67311 80.99836 95.36788
[8] 100.09100 88.83596 85.64991
> rowMin(tmp5,na.rm=TRUE)
[1] 60.57055 NA 54.92899 58.73409 55.60542 55.52615 57.72495 60.45803
[9] 55.47404 52.88341
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 112.88621 69.78667 70.36600 69.97924 70.20121 72.66645 76.74532
[8] 75.15070 73.80513 NaN 63.99685 68.81805 68.44170 68.74220
[15] 75.30805 73.22283 69.51248 73.72087 71.96987 76.59817
> colSums(tmp5,na.rm=TRUE)
[1] 1015.9759 628.0800 633.2940 629.8132 631.8109 653.9981 690.7079
[8] 676.3563 664.2462 0.0000 575.9717 619.3625 615.9753 618.6798
[15] 677.7724 659.0055 625.6123 663.4878 647.7288 689.3835
> colVars(tmp5,na.rm=TRUE)
[1] 17675.32740 60.60269 76.87683 171.75020 67.36500 66.07487
[7] 129.87585 116.17751 49.28862 NA 43.37160 120.24299
[13] 73.43566 52.93061 41.35887 91.28982 88.18816 25.17460
[19] 87.61039 153.97044
> colSd(tmp5,na.rm=TRUE)
[1] 132.948589 7.784773 8.767943 13.105350 8.207619 8.128645
[7] 11.396309 10.778567 7.020586 NA 6.585711 10.965536
[13] 8.569461 7.275343 6.431087 9.554571 9.390855 5.017429
[19] 9.360042 12.408483
> colMax(tmp5,na.rm=TRUE)
[1] 466.55404 84.82195 85.64991 98.30501 82.48884 85.90660 90.61234
[8] 95.36788 86.05449 -Inf 75.07126 86.32731 86.86380 77.63746
[15] 84.41897 87.11508 88.83596 81.49968 93.36382 100.09100
> colMin(tmp5,na.rm=TRUE)
[1] 55.47404 60.61156 59.18754 52.88341 60.70127 63.27835 60.38378 55.56668
[9] 65.07828 Inf 54.92899 55.60542 55.52615 56.71332 64.54693 59.73173
[17] 58.73409 67.68637 63.02185 63.14455
>
>
>
>
> 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] 270.8242 140.6626 396.0049 190.9865 275.6320 247.1112 151.2192 336.8009
[9] 347.9787 361.1729
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 270.8242 140.6626 396.0049 190.9865 275.6320 247.1112 151.2192 336.8009
[9] 347.9787 361.1729
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] 2.842171e-14 -1.705303e-13 -5.684342e-14 -1.989520e-13 -1.136868e-13
[6] 5.684342e-14 0.000000e+00 5.684342e-14 -8.526513e-14 0.000000e+00
[11] 0.000000e+00 1.705303e-13 -9.947598e-14 4.263256e-14 -1.278977e-13
[16] -1.136868e-13 -1.136868e-13 4.263256e-14 -5.684342e-14 7.105427e-14
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
2 3
4 3
1 2
7 13
3 5
8 2
7 14
7 16
4 19
4 17
9 5
8 19
5 14
5 3
4 18
3 10
6 10
9 15
6 17
10 14
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] 2.630338
> Min(tmp)
[1] -2.168635
> mean(tmp)
[1] 0.09362162
> Sum(tmp)
[1] 9.362162
> Var(tmp)
[1] 1.060036
>
> rowMeans(tmp)
[1] 0.09362162
> rowSums(tmp)
[1] 9.362162
> rowVars(tmp)
[1] 1.060036
> rowSd(tmp)
[1] 1.02958
> rowMax(tmp)
[1] 2.630338
> rowMin(tmp)
[1] -2.168635
>
> colMeans(tmp)
[1] 1.77826164 -0.20901594 0.03426128 -0.31253462 0.77799407 0.36157945
[7] 0.73464052 -0.13936457 -0.51500973 -0.72199862 2.15560868 0.30621796
[13] -0.67230130 1.43709946 -1.36012901 0.04658689 -0.01034769 -1.19815847
[19] 0.77652916 0.29534697 -0.46700533 -2.03138639 -1.18229877 -1.11183296
[25] -0.65948964 0.05478557 0.61827290 2.06499232 0.90871857 -0.35177090
[31] -1.28547065 -0.42776708 1.33754291 -1.01002976 -0.24055733 0.56108702
[37] -0.70509906 0.32741515 1.39263538 0.59361315 1.64067639 -1.81768838
[43] 0.51863468 -0.23512471 1.80012032 0.53243799 0.03637735 -0.65235246
[49] -0.94521449 -0.02567047 -0.62669738 0.65463787 2.43251341 -0.39500587
[55] 0.53353382 -1.81845241 -0.49826655 -0.83361541 0.91962162 -0.29777201
[61] -1.30923721 0.46318156 -0.72947426 2.63033760 -0.12095588 -0.60718876
[67] 1.53071372 0.85753994 2.14267890 1.80797926 -0.23784394 -0.08610658
[73] 1.00470604 -0.89912976 -1.11954175 1.20178063 0.64921975 0.64158749
[79] -0.47538227 -0.09820754 -2.16863544 0.29795299 1.62377166 -2.01672755
[85] -0.39516789 0.65682454 1.03921739 0.14743889 0.08607478 0.67351254
[91] 0.82713575 -1.10403178 0.39631815 -0.67420178 0.32963465 0.86905475
[97] 0.22706181 -1.04918372 -0.46200984 -0.06284946
> colSums(tmp)
[1] 1.77826164 -0.20901594 0.03426128 -0.31253462 0.77799407 0.36157945
[7] 0.73464052 -0.13936457 -0.51500973 -0.72199862 2.15560868 0.30621796
[13] -0.67230130 1.43709946 -1.36012901 0.04658689 -0.01034769 -1.19815847
[19] 0.77652916 0.29534697 -0.46700533 -2.03138639 -1.18229877 -1.11183296
[25] -0.65948964 0.05478557 0.61827290 2.06499232 0.90871857 -0.35177090
[31] -1.28547065 -0.42776708 1.33754291 -1.01002976 -0.24055733 0.56108702
[37] -0.70509906 0.32741515 1.39263538 0.59361315 1.64067639 -1.81768838
[43] 0.51863468 -0.23512471 1.80012032 0.53243799 0.03637735 -0.65235246
[49] -0.94521449 -0.02567047 -0.62669738 0.65463787 2.43251341 -0.39500587
[55] 0.53353382 -1.81845241 -0.49826655 -0.83361541 0.91962162 -0.29777201
[61] -1.30923721 0.46318156 -0.72947426 2.63033760 -0.12095588 -0.60718876
[67] 1.53071372 0.85753994 2.14267890 1.80797926 -0.23784394 -0.08610658
[73] 1.00470604 -0.89912976 -1.11954175 1.20178063 0.64921975 0.64158749
[79] -0.47538227 -0.09820754 -2.16863544 0.29795299 1.62377166 -2.01672755
[85] -0.39516789 0.65682454 1.03921739 0.14743889 0.08607478 0.67351254
[91] 0.82713575 -1.10403178 0.39631815 -0.67420178 0.32963465 0.86905475
[97] 0.22706181 -1.04918372 -0.46200984 -0.06284946
> 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] 1.77826164 -0.20901594 0.03426128 -0.31253462 0.77799407 0.36157945
[7] 0.73464052 -0.13936457 -0.51500973 -0.72199862 2.15560868 0.30621796
[13] -0.67230130 1.43709946 -1.36012901 0.04658689 -0.01034769 -1.19815847
[19] 0.77652916 0.29534697 -0.46700533 -2.03138639 -1.18229877 -1.11183296
[25] -0.65948964 0.05478557 0.61827290 2.06499232 0.90871857 -0.35177090
[31] -1.28547065 -0.42776708 1.33754291 -1.01002976 -0.24055733 0.56108702
[37] -0.70509906 0.32741515 1.39263538 0.59361315 1.64067639 -1.81768838
[43] 0.51863468 -0.23512471 1.80012032 0.53243799 0.03637735 -0.65235246
[49] -0.94521449 -0.02567047 -0.62669738 0.65463787 2.43251341 -0.39500587
[55] 0.53353382 -1.81845241 -0.49826655 -0.83361541 0.91962162 -0.29777201
[61] -1.30923721 0.46318156 -0.72947426 2.63033760 -0.12095588 -0.60718876
[67] 1.53071372 0.85753994 2.14267890 1.80797926 -0.23784394 -0.08610658
[73] 1.00470604 -0.89912976 -1.11954175 1.20178063 0.64921975 0.64158749
[79] -0.47538227 -0.09820754 -2.16863544 0.29795299 1.62377166 -2.01672755
[85] -0.39516789 0.65682454 1.03921739 0.14743889 0.08607478 0.67351254
[91] 0.82713575 -1.10403178 0.39631815 -0.67420178 0.32963465 0.86905475
[97] 0.22706181 -1.04918372 -0.46200984 -0.06284946
> colMin(tmp)
[1] 1.77826164 -0.20901594 0.03426128 -0.31253462 0.77799407 0.36157945
[7] 0.73464052 -0.13936457 -0.51500973 -0.72199862 2.15560868 0.30621796
[13] -0.67230130 1.43709946 -1.36012901 0.04658689 -0.01034769 -1.19815847
[19] 0.77652916 0.29534697 -0.46700533 -2.03138639 -1.18229877 -1.11183296
[25] -0.65948964 0.05478557 0.61827290 2.06499232 0.90871857 -0.35177090
[31] -1.28547065 -0.42776708 1.33754291 -1.01002976 -0.24055733 0.56108702
[37] -0.70509906 0.32741515 1.39263538 0.59361315 1.64067639 -1.81768838
[43] 0.51863468 -0.23512471 1.80012032 0.53243799 0.03637735 -0.65235246
[49] -0.94521449 -0.02567047 -0.62669738 0.65463787 2.43251341 -0.39500587
[55] 0.53353382 -1.81845241 -0.49826655 -0.83361541 0.91962162 -0.29777201
[61] -1.30923721 0.46318156 -0.72947426 2.63033760 -0.12095588 -0.60718876
[67] 1.53071372 0.85753994 2.14267890 1.80797926 -0.23784394 -0.08610658
[73] 1.00470604 -0.89912976 -1.11954175 1.20178063 0.64921975 0.64158749
[79] -0.47538227 -0.09820754 -2.16863544 0.29795299 1.62377166 -2.01672755
[85] -0.39516789 0.65682454 1.03921739 0.14743889 0.08607478 0.67351254
[91] 0.82713575 -1.10403178 0.39631815 -0.67420178 0.32963465 0.86905475
[97] 0.22706181 -1.04918372 -0.46200984 -0.06284946
> colMedians(tmp)
[1] 1.77826164 -0.20901594 0.03426128 -0.31253462 0.77799407 0.36157945
[7] 0.73464052 -0.13936457 -0.51500973 -0.72199862 2.15560868 0.30621796
[13] -0.67230130 1.43709946 -1.36012901 0.04658689 -0.01034769 -1.19815847
[19] 0.77652916 0.29534697 -0.46700533 -2.03138639 -1.18229877 -1.11183296
[25] -0.65948964 0.05478557 0.61827290 2.06499232 0.90871857 -0.35177090
[31] -1.28547065 -0.42776708 1.33754291 -1.01002976 -0.24055733 0.56108702
[37] -0.70509906 0.32741515 1.39263538 0.59361315 1.64067639 -1.81768838
[43] 0.51863468 -0.23512471 1.80012032 0.53243799 0.03637735 -0.65235246
[49] -0.94521449 -0.02567047 -0.62669738 0.65463787 2.43251341 -0.39500587
[55] 0.53353382 -1.81845241 -0.49826655 -0.83361541 0.91962162 -0.29777201
[61] -1.30923721 0.46318156 -0.72947426 2.63033760 -0.12095588 -0.60718876
[67] 1.53071372 0.85753994 2.14267890 1.80797926 -0.23784394 -0.08610658
[73] 1.00470604 -0.89912976 -1.11954175 1.20178063 0.64921975 0.64158749
[79] -0.47538227 -0.09820754 -2.16863544 0.29795299 1.62377166 -2.01672755
[85] -0.39516789 0.65682454 1.03921739 0.14743889 0.08607478 0.67351254
[91] 0.82713575 -1.10403178 0.39631815 -0.67420178 0.32963465 0.86905475
[97] 0.22706181 -1.04918372 -0.46200984 -0.06284946
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 1.778262 -0.2090159 0.03426128 -0.3125346 0.7779941 0.3615794 0.7346405
[2,] 1.778262 -0.2090159 0.03426128 -0.3125346 0.7779941 0.3615794 0.7346405
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.1393646 -0.5150097 -0.7219986 2.155609 0.306218 -0.6723013 1.437099
[2,] -0.1393646 -0.5150097 -0.7219986 2.155609 0.306218 -0.6723013 1.437099
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -1.360129 0.04658689 -0.01034769 -1.198158 0.7765292 0.295347 -0.4670053
[2,] -1.360129 0.04658689 -0.01034769 -1.198158 0.7765292 0.295347 -0.4670053
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -2.031386 -1.182299 -1.111833 -0.6594896 0.05478557 0.6182729 2.064992
[2,] -2.031386 -1.182299 -1.111833 -0.6594896 0.05478557 0.6182729 2.064992
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.9087186 -0.3517709 -1.285471 -0.4277671 1.337543 -1.01003 -0.2405573
[2,] 0.9087186 -0.3517709 -1.285471 -0.4277671 1.337543 -1.01003 -0.2405573
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.561087 -0.7050991 0.3274151 1.392635 0.5936132 1.640676 -1.817688
[2,] 0.561087 -0.7050991 0.3274151 1.392635 0.5936132 1.640676 -1.817688
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.5186347 -0.2351247 1.80012 0.532438 0.03637735 -0.6523525 -0.9452145
[2,] 0.5186347 -0.2351247 1.80012 0.532438 0.03637735 -0.6523525 -0.9452145
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -0.02567047 -0.6266974 0.6546379 2.432513 -0.3950059 0.5335338 -1.818452
[2,] -0.02567047 -0.6266974 0.6546379 2.432513 -0.3950059 0.5335338 -1.818452
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -0.4982665 -0.8336154 0.9196216 -0.297772 -1.309237 0.4631816 -0.7294743
[2,] -0.4982665 -0.8336154 0.9196216 -0.297772 -1.309237 0.4631816 -0.7294743
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 2.630338 -0.1209559 -0.6071888 1.530714 0.8575399 2.142679 1.807979
[2,] 2.630338 -0.1209559 -0.6071888 1.530714 0.8575399 2.142679 1.807979
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -0.2378439 -0.08610658 1.004706 -0.8991298 -1.119542 1.201781 0.6492197
[2,] -0.2378439 -0.08610658 1.004706 -0.8991298 -1.119542 1.201781 0.6492197
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 0.6415875 -0.4753823 -0.09820754 -2.168635 0.297953 1.623772 -2.016728
[2,] 0.6415875 -0.4753823 -0.09820754 -2.168635 0.297953 1.623772 -2.016728
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -0.3951679 0.6568245 1.039217 0.1474389 0.08607478 0.6735125 0.8271357
[2,] -0.3951679 0.6568245 1.039217 0.1474389 0.08607478 0.6735125 0.8271357
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -1.104032 0.3963181 -0.6742018 0.3296346 0.8690548 0.2270618 -1.049184
[2,] -1.104032 0.3963181 -0.6742018 0.3296346 0.8690548 0.2270618 -1.049184
[,99] [,100]
[1,] -0.4620098 -0.06284946
[2,] -0.4620098 -0.06284946
>
>
> Max(tmp2)
[1] 2.937364
> Min(tmp2)
[1] -2.298268
> mean(tmp2)
[1] -0.003461012
> Sum(tmp2)
[1] -0.3461012
> Var(tmp2)
[1] 1.12252
>
> rowMeans(tmp2)
[1] 0.12149470 -0.59667453 0.63554977 -0.18726198 -0.16196812 -1.60567699
[7] -0.91818787 -0.12185247 -0.66077357 -2.19093360 1.12666737 -1.26697221
[13] -0.35128406 1.69408854 0.70668723 0.39595440 1.29298460 -1.05269593
[19] 0.93868777 -0.70868351 0.34709458 -1.08390295 0.30783437 0.56725657
[25] -0.16219037 0.30598716 0.19544007 2.45513763 -1.24627808 1.23815232
[31] 0.73717140 1.44070560 0.50940591 0.04200699 -0.37774337 -0.06107949
[37] 0.76682085 -0.06222677 -0.45994984 0.90223815 -1.28469393 2.73608413
[43] -0.87026187 0.24757069 -0.77932057 0.61394658 -1.15920164 1.40246458
[49] -0.41137086 -0.65373982 -1.44877995 -1.14027581 -0.77742999 1.28359798
[55] 0.86729408 0.04902258 -0.30750433 0.38587211 0.81397122 0.24687648
[61] -1.52866073 0.31003378 -0.73608841 -1.59361064 -1.22997401 0.55378530
[67] -1.92215888 -0.09845352 -1.22264329 -0.75570680 0.68351883 1.32270721
[73] 1.39224055 0.26279921 -0.40742472 1.17872419 0.52421812 -1.16968452
[79] -0.02808930 -0.45357662 0.77989689 -0.90159069 -0.88726498 -0.57055781
[85] 2.05957874 -2.29826771 -0.37118735 -0.27930916 -0.60721932 -1.42983665
[91] -0.78811224 1.99108180 0.28849245 0.24417419 2.93736390 -0.26069759
[97] 0.12745035 1.72482154 -0.98389631 0.53187107
> rowSums(tmp2)
[1] 0.12149470 -0.59667453 0.63554977 -0.18726198 -0.16196812 -1.60567699
[7] -0.91818787 -0.12185247 -0.66077357 -2.19093360 1.12666737 -1.26697221
[13] -0.35128406 1.69408854 0.70668723 0.39595440 1.29298460 -1.05269593
[19] 0.93868777 -0.70868351 0.34709458 -1.08390295 0.30783437 0.56725657
[25] -0.16219037 0.30598716 0.19544007 2.45513763 -1.24627808 1.23815232
[31] 0.73717140 1.44070560 0.50940591 0.04200699 -0.37774337 -0.06107949
[37] 0.76682085 -0.06222677 -0.45994984 0.90223815 -1.28469393 2.73608413
[43] -0.87026187 0.24757069 -0.77932057 0.61394658 -1.15920164 1.40246458
[49] -0.41137086 -0.65373982 -1.44877995 -1.14027581 -0.77742999 1.28359798
[55] 0.86729408 0.04902258 -0.30750433 0.38587211 0.81397122 0.24687648
[61] -1.52866073 0.31003378 -0.73608841 -1.59361064 -1.22997401 0.55378530
[67] -1.92215888 -0.09845352 -1.22264329 -0.75570680 0.68351883 1.32270721
[73] 1.39224055 0.26279921 -0.40742472 1.17872419 0.52421812 -1.16968452
[79] -0.02808930 -0.45357662 0.77989689 -0.90159069 -0.88726498 -0.57055781
[85] 2.05957874 -2.29826771 -0.37118735 -0.27930916 -0.60721932 -1.42983665
[91] -0.78811224 1.99108180 0.28849245 0.24417419 2.93736390 -0.26069759
[97] 0.12745035 1.72482154 -0.98389631 0.53187107
> 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] 0.12149470 -0.59667453 0.63554977 -0.18726198 -0.16196812 -1.60567699
[7] -0.91818787 -0.12185247 -0.66077357 -2.19093360 1.12666737 -1.26697221
[13] -0.35128406 1.69408854 0.70668723 0.39595440 1.29298460 -1.05269593
[19] 0.93868777 -0.70868351 0.34709458 -1.08390295 0.30783437 0.56725657
[25] -0.16219037 0.30598716 0.19544007 2.45513763 -1.24627808 1.23815232
[31] 0.73717140 1.44070560 0.50940591 0.04200699 -0.37774337 -0.06107949
[37] 0.76682085 -0.06222677 -0.45994984 0.90223815 -1.28469393 2.73608413
[43] -0.87026187 0.24757069 -0.77932057 0.61394658 -1.15920164 1.40246458
[49] -0.41137086 -0.65373982 -1.44877995 -1.14027581 -0.77742999 1.28359798
[55] 0.86729408 0.04902258 -0.30750433 0.38587211 0.81397122 0.24687648
[61] -1.52866073 0.31003378 -0.73608841 -1.59361064 -1.22997401 0.55378530
[67] -1.92215888 -0.09845352 -1.22264329 -0.75570680 0.68351883 1.32270721
[73] 1.39224055 0.26279921 -0.40742472 1.17872419 0.52421812 -1.16968452
[79] -0.02808930 -0.45357662 0.77989689 -0.90159069 -0.88726498 -0.57055781
[85] 2.05957874 -2.29826771 -0.37118735 -0.27930916 -0.60721932 -1.42983665
[91] -0.78811224 1.99108180 0.28849245 0.24417419 2.93736390 -0.26069759
[97] 0.12745035 1.72482154 -0.98389631 0.53187107
> rowMin(tmp2)
[1] 0.12149470 -0.59667453 0.63554977 -0.18726198 -0.16196812 -1.60567699
[7] -0.91818787 -0.12185247 -0.66077357 -2.19093360 1.12666737 -1.26697221
[13] -0.35128406 1.69408854 0.70668723 0.39595440 1.29298460 -1.05269593
[19] 0.93868777 -0.70868351 0.34709458 -1.08390295 0.30783437 0.56725657
[25] -0.16219037 0.30598716 0.19544007 2.45513763 -1.24627808 1.23815232
[31] 0.73717140 1.44070560 0.50940591 0.04200699 -0.37774337 -0.06107949
[37] 0.76682085 -0.06222677 -0.45994984 0.90223815 -1.28469393 2.73608413
[43] -0.87026187 0.24757069 -0.77932057 0.61394658 -1.15920164 1.40246458
[49] -0.41137086 -0.65373982 -1.44877995 -1.14027581 -0.77742999 1.28359798
[55] 0.86729408 0.04902258 -0.30750433 0.38587211 0.81397122 0.24687648
[61] -1.52866073 0.31003378 -0.73608841 -1.59361064 -1.22997401 0.55378530
[67] -1.92215888 -0.09845352 -1.22264329 -0.75570680 0.68351883 1.32270721
[73] 1.39224055 0.26279921 -0.40742472 1.17872419 0.52421812 -1.16968452
[79] -0.02808930 -0.45357662 0.77989689 -0.90159069 -0.88726498 -0.57055781
[85] 2.05957874 -2.29826771 -0.37118735 -0.27930916 -0.60721932 -1.42983665
[91] -0.78811224 1.99108180 0.28849245 0.24417419 2.93736390 -0.26069759
[97] 0.12745035 1.72482154 -0.98389631 0.53187107
>
> colMeans(tmp2)
[1] -0.003461012
> colSums(tmp2)
[1] -0.3461012
> colVars(tmp2)
[1] 1.12252
> colSd(tmp2)
[1] 1.05949
> colMax(tmp2)
[1] 2.937364
> colMin(tmp2)
[1] -2.298268
> colMedians(tmp2)
[1] -0.06165313
> colRanges(tmp2)
[,1]
[1,] -2.298268
[2,] 2.937364
>
> 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] 0.9453990 -1.6398342 1.5275645 -2.0304295 9.8478090 -1.9537001
[7] -4.8753028 0.8374111 -11.6730945 5.6090766
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.39046088
[2,] -0.59821679
[3,] 0.06256075
[4,] 0.83927308
[5,] 1.56683509
>
> rowApply(tmp,sum)
[1] 1.8037272 2.6651268 -1.3096132 1.9735284 0.7735761 0.8708039
[7] -5.8185917 -4.4059723 2.4514823 -2.4091685
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 9 7 4 3 5 4 10 2 6 7
[2,] 5 3 5 7 4 9 5 5 2 3
[3,] 6 6 9 6 2 6 1 8 7 8
[4,] 4 2 6 8 3 8 8 4 8 2
[5,] 7 10 7 10 10 10 3 9 10 5
[6,] 1 9 1 4 9 5 4 10 4 6
[7,] 2 8 2 2 6 7 7 1 3 4
[8,] 3 5 8 5 8 2 6 7 5 9
[9,] 10 1 3 1 1 1 2 3 1 1
[10,] 8 4 10 9 7 3 9 6 9 10
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -0.6930550 1.1641062 0.9589554 -5.4619246 0.7753789 3.9807598
[7] -0.8985752 -0.5555108 3.2859425 0.2354088 -0.7680854 -1.3969398
[13] 1.7799303 2.2903071 3.0915993 1.3724191 -0.2461151 0.2044007
[19] -0.3224514 2.0282402
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.98608268
[2,] -0.37045470
[3,] -0.18903550
[4,] -0.08912516
[5,] 0.94164306
>
> rowApply(tmp,sum)
[1] 9.007147 -3.365213 -4.412862 6.737990 2.857729
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 2 11 10 6 16
[2,] 12 4 12 9 20
[3,] 7 19 17 3 9
[4,] 3 2 15 1 1
[5,] 8 6 9 14 15
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.98608268 0.51046369 -0.03529608 -0.9196522 0.1086407 0.786911081
[2,] -0.18903550 -0.92941927 0.86405214 -1.4759441 -0.8404104 0.779450476
[3,] -0.08912516 -0.03373067 0.70215431 0.1820546 -0.1808641 -0.836043514
[4,] -0.37045470 0.03216855 -0.61931975 -1.2385246 0.7734134 3.245164941
[5,] 0.94164306 1.58462390 0.04736474 -2.0098583 0.9145993 0.005276773
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 2.2758441 1.2707430 0.42549875 0.39104291 -0.2296959 -0.8072116
[2,] -1.0771926 -0.2268057 1.89794364 0.09232925 0.8064633 -0.8941765
[3,] -0.7706305 -0.9194317 0.09958960 -0.85908718 -2.0713154 1.0699332
[4,] -0.1812060 0.2236422 0.79419686 1.00082968 1.2534457 -1.0084805
[5,] -1.1453903 -0.9036586 0.06871367 -0.38970584 -0.5269831 0.2429956
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.9474698 -0.36017724 2.37715602 0.68050297 -1.5447607 2.2486312
[2,] -2.2792330 0.34216129 0.34815126 0.03883631 0.7243174 -0.3892524
[3,] 1.2464068 0.07121569 0.70413184 -0.07598745 -0.4428191 -1.1760985
[4,] 0.7233316 1.21999459 -0.42438774 0.71671175 -0.2535293 -0.6149844
[5,] 1.1419551 1.01711274 0.08654789 0.01235553 1.2706766 0.1361048
[,19] [,20]
[1,] 1.4140420 0.4530773
[2,] -0.7599041 -0.1975443
[3,] -1.2784424 0.2452271
[4,] 0.4767082 0.9892697
[5,] -0.1748550 0.5382104
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-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-3.22-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-3.22-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-3.22-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 0.5471176 0.5990489 -1.058397 -2.223356 -0.7939639 0.7267729 0.02578209
col8 col9 col10 col11 col12 col13 col14
row1 -1.785389 -0.1516448 0.1032101 0.1058585 0.4450717 -1.241244 -0.9585729
col15 col16 col17 col18 col19 col20
row1 -0.848603 -2.033797 0.3192519 -0.6495496 0.6458707 -1.350165
> tmp[,"col10"]
col10
row1 0.1032101
row2 1.6621609
row3 -0.3197135
row4 0.1342723
row5 1.1781599
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 0.5471176 0.5990489 -1.0583972 -2.2233556 -0.7939639 0.7267729 0.02578209
row5 0.3867571 1.7148798 -0.3945576 -0.7445221 1.2034073 1.5394608 0.68772776
col8 col9 col10 col11 col12 col13 col14
row1 -1.785389 -0.1516448 0.1032101 0.1058585 0.4450717 -1.2412445 -0.9585729
row5 0.651784 0.2107809 1.1781599 0.9013924 0.4669779 -0.0889289 -0.2762579
col15 col16 col17 col18 col19 col20
row1 -0.848603 -2.033797 0.3192519 -0.6495496 0.6458707 -1.3501647
row5 0.183746 -1.024675 0.2155788 -0.4927255 0.4108159 0.5057168
> tmp[,c("col6","col20")]
col6 col20
row1 0.7267729 -1.3501647
row2 1.1040413 -0.4222542
row3 1.0683768 0.3283644
row4 -1.1615370 1.8504596
row5 1.5394608 0.5057168
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.7267729 -1.3501647
row5 1.5394608 0.5057168
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 52.63447 52.40121 50.53603 49.02211 50.98796 104.7426 49.018 49.71605
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.69912 50.01757 50.47407 50.09148 50.59523 49.9247 47.83006 50.74904
col17 col18 col19 col20
row1 47.24164 49.55025 49.91977 103.2141
> tmp[,"col10"]
col10
row1 50.01757
row2 31.22449
row3 30.29410
row4 31.05796
row5 50.98308
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 52.63447 52.40121 50.53603 49.02211 50.98796 104.7426 49.01800 49.71605
row5 48.53242 50.28020 50.67796 50.05965 50.60899 103.4411 49.71609 48.87907
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.69912 50.01757 50.47407 50.09148 50.59523 49.92470 47.83006 50.74904
row5 50.30814 50.98308 50.35359 49.31133 50.60917 49.24652 50.48600 48.15522
col17 col18 col19 col20
row1 47.24164 49.55025 49.91977 103.2141
row5 50.99091 50.39902 50.17436 105.8267
> tmp[,c("col6","col20")]
col6 col20
row1 104.74257 103.21410
row2 76.08825 76.45532
row3 74.85500 76.06916
row4 75.39796 76.22601
row5 103.44111 105.82673
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.7426 103.2141
row5 103.4411 105.8267
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.7426 103.2141
row5 103.4411 105.8267
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.9928034
[2,] 0.9948648
[3,] -0.4217847
[4,] -0.3769231
[5,] -0.9787058
> tmp[,c("col17","col7")]
col17 col7
[1,] 0.68794200 -0.03510972
[2,] -0.46065940 -0.33815410
[3,] 0.16286047 -0.13328438
[4,] -1.33399849 -0.83887489
[5,] -0.09461359 0.74586205
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -1.6897718 0.6258217
[2,] 0.5021036 -0.7363103
[3,] 0.4727020 -0.3823925
[4,] -0.4087652 -1.7392202
[5,] -1.7642469 -1.6571374
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -1.689772
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -1.6897718
[2,] 0.5021036
>
>
>
> 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 0.1143558 1.155725 0.7222836 0.5431301 0.1221271 -2.894832 0.6867369
row1 0.1169726 1.374647 0.8342037 1.0739037 0.3216356 -1.022350 -0.1939420
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row3 0.2716423 0.9295255 0.6640439 1.69692128 0.3002938 -0.4153386 0.3915233
row1 0.3612906 -2.0769913 2.0860072 0.01213109 1.2109907 -0.8934260 -0.3686141
[,15] [,16] [,17] [,18] [,19] [,20]
row3 -2.0893014 0.3886413 2.5643753 0.1522270 -1.3957879 0.002587226
row1 -0.8524827 -0.5478495 -0.6477832 0.1755722 -0.6421652 -0.625085737
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -1.744599 -0.5299658 1.135676 0.2240803 -1.375571 0.5708039 -1.088597
[,8] [,9] [,10]
row2 -0.3560342 -1.886366 -0.6783526
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -0.7723927 0.2949141 0.4466837 0.9035509 -0.4253134 -1.257879 0.7263463
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.542131 0.8069586 -1.23662 -0.4868603 -1.719193 0.2757881 1.488246
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -1.508604 0.1883839 -1.608886 -1.39036 0.9424588 -0.542216
>
>
> 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: 0x5843414200a0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM383b283c7f679d"
[2] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM383b28492e2bb6"
[3] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM383b28ab9e0a7"
[4] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM383b2842304794"
[5] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM383b288a87a91"
[6] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM383b28722a391b"
[7] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM383b28291aff52"
[8] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM383b28a8aa3bc"
[9] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM383b2870080c0e"
[10] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM383b2812938583"
[11] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM383b2834c175b5"
[12] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM383b288d0584e"
[13] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM383b2813dffe1d"
[14] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM383b282f88c940"
[15] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM383b28626d32eb"
>
>
> ### 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: 0x58434136e570>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x58434136e570>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x58434136e570>
> rowMedians(tmp)
[1] 0.195969249 0.394188446 0.124241104 0.047060095 0.128286857
[6] -0.459644102 -0.529803203 -0.203320977 -0.386628217 0.076904421
[11] -0.334733343 -0.064350009 0.525129522 0.256908812 0.021826932
[16] 0.561444320 -0.324047246 0.086904591 0.707960017 0.514551241
[21] -0.380266535 -0.356662985 -0.298596649 0.085331586 -0.177911344
[26] -0.384134233 -0.386311772 -0.311917131 -0.032143832 -0.333588125
[31] -0.337978290 0.090013935 -0.059773663 -0.145925702 -0.126059303
[36] -0.003070350 0.535637905 0.461759687 0.282773622 0.517506308
[41] 0.023368673 -0.185435986 -0.258223321 -0.228626672 -0.031865105
[46] 0.282618337 -0.452316953 0.281904938 -0.140108505 -0.060162369
[51] 0.086157944 0.479604002 -0.219507908 -0.589948758 -0.011404339
[56] -0.480209072 0.497938260 -0.068432747 0.228336027 0.378831648
[61] 0.047839400 -0.238797821 -0.155995230 -0.419412877 0.127038524
[66] -0.472998666 0.076664151 -0.338492150 0.189950033 0.072104754
[71] -0.319086346 0.182733925 -0.284983287 -0.659829628 0.629155747
[76] -0.509837243 0.727943634 0.539972885 0.164424644 -0.010510082
[81] -0.214083237 0.049022911 -0.594169255 -0.392291833 -0.132631116
[86] -0.617580151 0.302232501 0.274712058 0.339087819 -0.405280922
[91] 0.431745007 -0.117398567 0.204898061 -0.158201557 0.282711757
[96] 0.138144469 0.352329397 -0.321553469 0.362284130 0.033814152
[101] 0.104653023 0.849766393 -0.580643845 0.577944880 -0.314543882
[106] 0.061473722 0.240887926 -0.233374530 0.008125570 0.393097464
[111] -0.132652061 0.361302768 -0.207342677 0.454815340 0.583840695
[116] -0.014231673 0.121871929 0.139101164 -0.609991604 -0.166280860
[121] 0.509533358 -0.051282946 -0.115454120 -0.296222348 -0.447578326
[126] -0.019378011 -0.356465477 -0.459999426 0.007971803 0.074607213
[131] -0.393440140 -0.124068091 0.398565028 -0.043052193 0.200572035
[136] 0.174305424 -0.125078496 -0.256554268 -0.193226415 -0.252133587
[141] -0.328304786 -0.357112347 0.328485062 -0.207593320 0.023295553
[146] 0.058047127 -0.131302778 0.140529043 -0.131877425 0.120133641
[151] -0.262878217 0.093022665 -0.068932181 -0.291772066 -0.069544220
[156] -0.308029150 0.132712473 -0.554868078 0.415583894 -0.226746264
[161] 0.256194382 0.207460500 -0.319635345 -0.753134069 0.379619142
[166] -0.097443574 -0.087646327 0.081470554 0.170374486 -0.166806692
[171] -0.169177069 0.222301503 0.398808059 -0.478048858 0.598552593
[176] -0.122595499 -0.711675891 0.552383114 0.146951027 0.184497864
[181] 0.065142733 0.054738925 0.178291504 0.270305952 0.072057254
[186] 0.134563508 -0.129426536 -0.630212857 0.004373192 -0.116357201
[191] 0.246522989 -0.233488243 0.011024294 0.702178669 -0.034943737
[196] -0.137067642 -0.152376316 0.632059866 -0.231169923 0.239668915
[201] -0.266651238 0.480631318 0.126512086 0.698974155 0.210052763
[206] -0.034049935 0.315171183 -0.248079269 0.346690726 -0.236444264
[211] -0.505016156 -0.333519471 -0.238512692 -0.372729014 0.794425687
[216] 0.094309749 -0.197786917 -0.040508171 -0.266314263 0.546039228
[221] -0.476140067 0.088961883 0.198554431 0.117822357 -0.094089609
[226] -0.045893655 0.227422892 0.058924964 0.064703067 0.132748369
>
> proc.time()
user system elapsed
1.258 0.673 1.915
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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: 0x638316301370>
> .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: 0x638316301370>
> .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: 0x638316301370>
> .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: 0x638316301370>
> 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: 0x6383162e91c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6383162e91c0>
> .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: 0x6383162e91c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6383162e91c0>
> .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: 0x6383162e91c0>
> 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: 0x6383165cc120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6383165cc120>
> .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: 0x6383165cc120>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x6383165cc120>
> .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: 0x6383165cc120>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x6383165cc120>
> .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: 0x6383165cc120>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x6383165cc120>
> .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: 0x6383165cc120>
> 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: 0x63831531c390>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x63831531c390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x63831531c390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x63831531c390>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile383b6257a2032d" "BufferedMatrixFile383b62aa36688"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile383b6257a2032d" "BufferedMatrixFile383b62aa36688"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x6383152133d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x6383152133d0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x6383152133d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x6383152133d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x6383152133d0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x6383152133d0>
> .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: 0x638316d48fa0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x638316d48fa0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x638316d48fa0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x638316d48fa0>
> 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: 0x638315520ff0>
> .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: 0x638315520ff0>
> rm(P)
>
> proc.time()
user system elapsed
0.250 0.044 0.282
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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Platform: x86_64-pc-linux-gnu
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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
0.231 0.045 0.266