Ben Bolstad
| Snapshot Date: 2026-02-26 13:40 -0500 (Thu, 26 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: devel |
| git_last_commit: ecdbf23 |
| git_last_commit_date: 2025-10-29 09:58:55 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-27 11:32 -0500 (Fri, 27 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4877 |
| 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 255/2357 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.75.0 (landing page) Ben Bolstad
| nebbiolo1 | 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: 1.75.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BufferedMatrix_1.75.0.tar.gz |
| StartedAt: 2026-02-26 21:50:59 -0500 (Thu, 26 Feb 2026) |
| EndedAt: 2026-02-26 21:51:25 -0500 (Thu, 26 Feb 2026) |
| EllapsedTime: 25.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BufferedMatrix_1.75.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘1.75.0’
* 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 ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ...* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.75.0’
** 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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-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-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-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 Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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
0.248 0.053 0.290
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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-3.23-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 478920 25.6 1048721 56.1 639242 34.2
Vcells 885815 6.8 8388608 64.0 2083259 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] "Thu Feb 26 21:51:14 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] "Thu Feb 26 21:51:15 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: 0x6116c06bac10>
>
>
>
> 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] "Thu Feb 26 21:51:15 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] "Thu Feb 26 21:51:15 2026"
>
> ColMode(tmp2)
<pointer: 0x6116c06bac10>
>
>
>
> ### 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,] 100.0918551 -1.39361785 -1.6719121 1.01063263
[2,] 0.6661182 1.75341952 0.5113443 0.62245194
[3,] -0.1775876 0.09884394 0.3695898 0.72100207
[4,] 0.0461528 -0.92251999 -2.1842854 -0.07890257
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-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,] 100.0918551 1.39361785 1.6719121 1.01063263
[2,] 0.6661182 1.75341952 0.5113443 0.62245194
[3,] 0.1775876 0.09884394 0.3695898 0.72100207
[4,] 0.0461528 0.92251999 2.1842854 0.07890257
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-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,] 10.0045917 1.1805159 1.2930244 1.0053023
[2,] 0.8161607 1.3241675 0.7150834 0.7889562
[3,] 0.4214114 0.3143946 0.6079390 0.8491184
[4,] 0.2148320 0.9604790 1.4779328 0.2808960
>
> 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-3.23-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,] 225.13777 38.19878 39.60216 36.06366
[2,] 33.82772 39.99509 32.66218 33.51201
[3,] 29.39170 28.24279 31.44898 34.21219
[4,] 27.19447 35.52731 41.96361 27.88786
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x6116c11a5820>
> exp(tmp5)
<pointer: 0x6116c11a5820>
> log(tmp5,2)
<pointer: 0x6116c11a5820>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 468.5948
> Min(tmp5)
[1] 53.91789
> mean(tmp5)
[1] 72.08462
> Sum(tmp5)
[1] 14416.92
> Var(tmp5)
[1] 873.2297
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 93.90755 66.65960 68.22063 69.87295 70.31487 70.95155 70.35810 74.55685
[9] 67.18807 68.81599
> rowSums(tmp5)
[1] 1878.151 1333.192 1364.413 1397.459 1406.297 1419.031 1407.162 1491.137
[9] 1343.761 1376.320
> rowVars(tmp5)
[1] 7891.96130 68.82633 84.02974 91.09406 61.17113 48.22787
[7] 70.41035 102.17370 59.95088 64.23216
> rowSd(tmp5)
[1] 88.836711 8.296163 9.166774 9.544321 7.821197 6.944629 8.391088
[8] 10.108101 7.742795 8.014497
> rowMax(tmp5)
[1] 468.59478 83.24455 93.02980 87.74213 80.16578 84.64076 89.82004
[8] 98.60555 86.12816 88.66250
> rowMin(tmp5)
[1] 53.91789 54.57586 55.03244 55.11759 59.12462 60.38854 55.99773 57.54799
[9] 54.73606 56.21615
>
> colMeans(tmp5)
[1] 107.27530 71.27896 71.37939 66.64159 70.09854 69.17781 70.57652
[8] 68.86408 73.74158 68.80010 66.68666 70.28057 70.22888 69.70346
[15] 73.96708 71.82706 66.24254 74.22716 70.09376 70.60129
> colSums(tmp5)
[1] 1072.7530 712.7896 713.7939 666.4159 700.9854 691.7781 705.7652
[8] 688.6408 737.4158 688.0010 666.8666 702.8057 702.2888 697.0346
[15] 739.6708 718.2706 662.4254 742.2716 700.9376 706.0129
> colVars(tmp5)
[1] 16156.19106 49.05610 72.92735 71.92876 221.54035 54.85674
[7] 55.70246 80.03189 35.22157 75.10287 107.73571 87.51586
[13] 41.40892 73.70235 104.88940 107.06069 62.97336 48.72502
[19] 129.65545 118.81874
> colSd(tmp5)
[1] 127.107006 7.004006 8.539751 8.481083 14.884232 7.406534
[7] 7.463408 8.946054 5.934776 8.666191 10.379581 9.354991
[13] 6.434976 8.585007 10.241553 10.347013 7.935576 6.980331
[19] 11.386635 10.900401
> colMax(tmp5)
[1] 468.59478 83.24455 87.34176 78.83857 98.60555 78.79689 86.27846
[8] 87.64482 82.58242 84.46851 85.58043 89.25977 77.13803 87.74213
[15] 89.82004 86.12816 80.33623 88.66250 90.63787 84.64076
> colMin(tmp5)
[1] 56.60173 58.78367 62.27459 55.96015 53.91789 59.46168 59.60615 57.68348
[9] 66.10625 59.46249 54.57586 58.59928 55.03244 60.38854 60.18244 57.67550
[17] 55.99773 66.33064 55.11759 54.73606
>
>
> ### 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] 93.90755 66.65960 68.22063 69.87295 70.31487 NA 70.35810 74.55685
[9] 67.18807 68.81599
> rowSums(tmp5)
[1] 1878.151 1333.192 1364.413 1397.459 1406.297 NA 1407.162 1491.137
[9] 1343.761 1376.320
> rowVars(tmp5)
[1] 7891.96130 68.82633 84.02974 91.09406 61.17113 49.41095
[7] 70.41035 102.17370 59.95088 64.23216
> rowSd(tmp5)
[1] 88.836711 8.296163 9.166774 9.544321 7.821197 7.029292 8.391088
[8] 10.108101 7.742795 8.014497
> rowMax(tmp5)
[1] 468.59478 83.24455 93.02980 87.74213 80.16578 NA 89.82004
[8] 98.60555 86.12816 88.66250
> rowMin(tmp5)
[1] 53.91789 54.57586 55.03244 55.11759 59.12462 NA 55.99773 57.54799
[9] 54.73606 56.21615
>
> colMeans(tmp5)
[1] 107.27530 71.27896 71.37939 66.64159 70.09854 69.17781 NA
[8] 68.86408 73.74158 68.80010 66.68666 70.28057 70.22888 69.70346
[15] 73.96708 71.82706 66.24254 74.22716 70.09376 70.60129
> colSums(tmp5)
[1] 1072.7530 712.7896 713.7939 666.4159 700.9854 691.7781 NA
[8] 688.6408 737.4158 688.0010 666.8666 702.8057 702.2888 697.0346
[15] 739.6708 718.2706 662.4254 742.2716 700.9376 706.0129
> colVars(tmp5)
[1] 16156.19106 49.05610 72.92735 71.92876 221.54035 54.85674
[7] NA 80.03189 35.22157 75.10287 107.73571 87.51586
[13] 41.40892 73.70235 104.88940 107.06069 62.97336 48.72502
[19] 129.65545 118.81874
> colSd(tmp5)
[1] 127.107006 7.004006 8.539751 8.481083 14.884232 7.406534
[7] NA 8.946054 5.934776 8.666191 10.379581 9.354991
[13] 6.434976 8.585007 10.241553 10.347013 7.935576 6.980331
[19] 11.386635 10.900401
> colMax(tmp5)
[1] 468.59478 83.24455 87.34176 78.83857 98.60555 78.79689 NA
[8] 87.64482 82.58242 84.46851 85.58043 89.25977 77.13803 87.74213
[15] 89.82004 86.12816 80.33623 88.66250 90.63787 84.64076
> colMin(tmp5)
[1] 56.60173 58.78367 62.27459 55.96015 53.91789 59.46168 NA 57.68348
[9] 66.10625 59.46249 54.57586 58.59928 55.03244 60.38854 60.18244 57.67550
[17] 55.99773 66.33064 55.11759 54.73606
>
> Max(tmp5,na.rm=TRUE)
[1] 468.5948
> Min(tmp5,na.rm=TRUE)
[1] 53.91789
> mean(tmp5,na.rm=TRUE)
[1] 72.06489
> Sum(tmp5,na.rm=TRUE)
[1] 14340.91
> Var(tmp5,na.rm=TRUE)
[1] 877.5618
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 93.90755 66.65960 68.22063 69.87295 70.31487 70.68533 70.35810 74.55685
[9] 67.18807 68.81599
> rowSums(tmp5,na.rm=TRUE)
[1] 1878.151 1333.192 1364.413 1397.459 1406.297 1343.021 1407.162 1491.137
[9] 1343.761 1376.320
> rowVars(tmp5,na.rm=TRUE)
[1] 7891.96130 68.82633 84.02974 91.09406 61.17113 49.41095
[7] 70.41035 102.17370 59.95088 64.23216
> rowSd(tmp5,na.rm=TRUE)
[1] 88.836711 8.296163 9.166774 9.544321 7.821197 7.029292 8.391088
[8] 10.108101 7.742795 8.014497
> rowMax(tmp5,na.rm=TRUE)
[1] 468.59478 83.24455 93.02980 87.74213 80.16578 84.64076 89.82004
[8] 98.60555 86.12816 88.66250
> rowMin(tmp5,na.rm=TRUE)
[1] 53.91789 54.57586 55.03244 55.11759 59.12462 60.38854 55.99773 57.54799
[9] 54.73606 56.21615
>
> colMeans(tmp5,na.rm=TRUE)
[1] 107.27530 71.27896 71.37939 66.64159 70.09854 69.17781 69.97282
[8] 68.86408 73.74158 68.80010 66.68666 70.28057 70.22888 69.70346
[15] 73.96708 71.82706 66.24254 74.22716 70.09376 70.60129
> colSums(tmp5,na.rm=TRUE)
[1] 1072.7530 712.7896 713.7939 666.4159 700.9854 691.7781 629.7554
[8] 688.6408 737.4158 688.0010 666.8666 702.8057 702.2888 697.0346
[15] 739.6708 718.2706 662.4254 742.2716 700.9376 706.0129
> colVars(tmp5,na.rm=TRUE)
[1] 16156.19106 49.05610 72.92735 71.92876 221.54035 54.85674
[7] 58.56518 80.03189 35.22157 75.10287 107.73571 87.51586
[13] 41.40892 73.70235 104.88940 107.06069 62.97336 48.72502
[19] 129.65545 118.81874
> colSd(tmp5,na.rm=TRUE)
[1] 127.107006 7.004006 8.539751 8.481083 14.884232 7.406534
[7] 7.652789 8.946054 5.934776 8.666191 10.379581 9.354991
[13] 6.434976 8.585007 10.241553 10.347013 7.935576 6.980331
[19] 11.386635 10.900401
> colMax(tmp5,na.rm=TRUE)
[1] 468.59478 83.24455 87.34176 78.83857 98.60555 78.79689 86.27846
[8] 87.64482 82.58242 84.46851 85.58043 89.25977 77.13803 87.74213
[15] 89.82004 86.12816 80.33623 88.66250 90.63787 84.64076
> colMin(tmp5,na.rm=TRUE)
[1] 56.60173 58.78367 62.27459 55.96015 53.91789 59.46168 59.60615 57.68348
[9] 66.10625 59.46249 54.57586 58.59928 55.03244 60.38854 60.18244 57.67550
[17] 55.99773 66.33064 55.11759 54.73606
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 93.90755 66.65960 68.22063 69.87295 70.31487 NaN 70.35810 74.55685
[9] 67.18807 68.81599
> rowSums(tmp5,na.rm=TRUE)
[1] 1878.151 1333.192 1364.413 1397.459 1406.297 0.000 1407.162 1491.137
[9] 1343.761 1376.320
> rowVars(tmp5,na.rm=TRUE)
[1] 7891.96130 68.82633 84.02974 91.09406 61.17113 NA
[7] 70.41035 102.17370 59.95088 64.23216
> rowSd(tmp5,na.rm=TRUE)
[1] 88.836711 8.296163 9.166774 9.544321 7.821197 NA 8.391088
[8] 10.108101 7.742795 8.014497
> rowMax(tmp5,na.rm=TRUE)
[1] 468.59478 83.24455 93.02980 87.74213 80.16578 NA 89.82004
[8] 98.60555 86.12816 88.66250
> rowMin(tmp5,na.rm=TRUE)
[1] 53.91789 54.57586 55.03244 55.11759 59.12462 NA 55.99773 57.54799
[9] 54.73606 56.21615
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 112.15057 71.10800 72.29438 65.71258 70.58741 68.39196 NaN
[8] 69.74296 73.96529 67.95515 66.10297 70.91101 70.43336 70.73845
[15] 73.22730 70.91308 66.04872 74.31766 70.59524 69.04135
> colSums(tmp5,na.rm=TRUE)
[1] 1009.3551 639.9720 650.6494 591.4132 635.2867 615.5277 0.0000
[8] 627.6867 665.6876 611.5964 594.9268 638.1991 633.9002 636.6461
[15] 659.0457 638.2177 594.4384 668.8589 635.3572 621.3721
> colVars(tmp5,na.rm=TRUE)
[1] 17908.32186 54.85930 72.62479 71.21026 246.54429 54.76639
[7] NA 81.34595 39.06125 76.45890 117.36990 93.98391
[13] 46.11464 70.86406 111.84380 111.04542 70.42241 54.72352
[19] 143.03318 106.29514
> colSd(tmp5,na.rm=TRUE)
[1] 133.821978 7.406706 8.522018 8.438617 15.701729 7.400432
[7] NA 9.019199 6.249900 8.744078 10.833739 9.694530
[13] 6.790776 8.418079 10.575623 10.537809 8.391806 7.397535
[19] 11.959648 10.309953
> colMax(tmp5,na.rm=TRUE)
[1] 468.59478 83.24455 87.34176 78.83857 98.60555 78.79689 -Inf
[8] 87.64482 82.58242 84.46851 85.58043 89.25977 77.13803 87.74213
[15] 89.82004 86.12816 80.33623 88.66250 90.63787 82.59486
> colMin(tmp5,na.rm=TRUE)
[1] 56.60173 58.78367 62.27459 55.96015 53.91789 59.46168 Inf 57.68348
[9] 66.10625 59.46249 54.57586 58.59928 55.03244 61.53296 60.18244 57.67550
[17] 55.99773 66.33064 55.11759 54.73606
>
>
>
>
> 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] 313.33014 254.25234 233.12207 97.88401 360.61645 331.45987 290.85125
[8] 301.49611 304.89611 251.65194
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 313.33014 254.25234 233.12207 97.88401 360.61645 331.45987 290.85125
[8] 301.49611 304.89611 251.65194
>
>
>
> 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] 1.136868e-13 -1.705303e-13 -2.842171e-13 -1.421085e-14 -1.136868e-13
[6] -2.557954e-13 1.136868e-13 -5.684342e-14 -5.684342e-14 -5.684342e-14
[11] 0.000000e+00 5.684342e-14 -5.684342e-14 -1.136868e-13 -5.684342e-14
[16] 2.273737e-13 4.263256e-14 -2.131628e-13 -5.684342e-14 -1.136868e-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)
+ }
2 10
7 17
4 19
4 3
3 9
1 6
7 6
10 8
2 11
5 8
1 4
8 19
9 14
9 9
2 9
9 7
3 12
1 11
5 3
9 8
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] 2.016845
> Min(tmp)
[1] -2.154864
> mean(tmp)
[1] -0.07495148
> Sum(tmp)
[1] -7.495148
> Var(tmp)
[1] 0.8004721
>
> rowMeans(tmp)
[1] -0.07495148
> rowSums(tmp)
[1] -7.495148
> rowVars(tmp)
[1] 0.8004721
> rowSd(tmp)
[1] 0.8946911
> rowMax(tmp)
[1] 2.016845
> rowMin(tmp)
[1] -2.154864
>
> colMeans(tmp)
[1] 0.07534757 -0.11062768 -0.25384825 0.81737808 -1.12565192 0.72487247
[7] 0.63823291 -0.30708462 -0.77730292 -0.19392631 0.27645116 -1.68739637
[13] 0.47124823 0.16788624 0.79804352 -0.18207134 1.69969081 -0.12653931
[19] 0.81910839 -0.34468753 -1.24829534 -0.68243626 -0.98744283 -0.14840811
[25] 0.56240004 0.51450528 0.45500499 0.82405315 -0.61428326 0.65276217
[31] 0.57833383 0.51893407 0.14541248 -1.55217026 0.92821683 -0.03062525
[37] 0.23838969 -0.49702727 0.04197453 -2.15220526 -1.01596916 -1.15148292
[43] -0.15027994 0.15490784 -0.40574101 0.73039861 -0.27039190 -1.16236298
[49] -0.32633569 -0.79952487 -0.94876346 -0.13089435 0.43214597 -0.56818921
[55] 2.01684508 -0.82919707 0.85473125 1.64459660 1.27949264 0.35604287
[61] -0.36903214 -2.11558527 -0.92383611 -2.15486428 0.16846347 -0.69597146
[67] -0.47219250 -0.14970865 -0.07834935 -1.54346880 1.52148548 -0.11910773
[73] 0.75005270 -1.51437805 0.47413169 0.95331461 1.83751031 0.19987434
[79] 0.05371480 -0.64942769 -0.53728274 -0.21584294 -0.14085315 -0.23399484
[85] -1.69830689 -0.63909399 -0.76948296 0.32579628 -0.25839902 1.28043837
[91] -0.31170169 0.13348002 -1.46557316 0.86365946 -0.27565459 0.37554626
[97] 1.89230923 -0.34808095 1.09947815 -0.38045866
> colSums(tmp)
[1] 0.07534757 -0.11062768 -0.25384825 0.81737808 -1.12565192 0.72487247
[7] 0.63823291 -0.30708462 -0.77730292 -0.19392631 0.27645116 -1.68739637
[13] 0.47124823 0.16788624 0.79804352 -0.18207134 1.69969081 -0.12653931
[19] 0.81910839 -0.34468753 -1.24829534 -0.68243626 -0.98744283 -0.14840811
[25] 0.56240004 0.51450528 0.45500499 0.82405315 -0.61428326 0.65276217
[31] 0.57833383 0.51893407 0.14541248 -1.55217026 0.92821683 -0.03062525
[37] 0.23838969 -0.49702727 0.04197453 -2.15220526 -1.01596916 -1.15148292
[43] -0.15027994 0.15490784 -0.40574101 0.73039861 -0.27039190 -1.16236298
[49] -0.32633569 -0.79952487 -0.94876346 -0.13089435 0.43214597 -0.56818921
[55] 2.01684508 -0.82919707 0.85473125 1.64459660 1.27949264 0.35604287
[61] -0.36903214 -2.11558527 -0.92383611 -2.15486428 0.16846347 -0.69597146
[67] -0.47219250 -0.14970865 -0.07834935 -1.54346880 1.52148548 -0.11910773
[73] 0.75005270 -1.51437805 0.47413169 0.95331461 1.83751031 0.19987434
[79] 0.05371480 -0.64942769 -0.53728274 -0.21584294 -0.14085315 -0.23399484
[85] -1.69830689 -0.63909399 -0.76948296 0.32579628 -0.25839902 1.28043837
[91] -0.31170169 0.13348002 -1.46557316 0.86365946 -0.27565459 0.37554626
[97] 1.89230923 -0.34808095 1.09947815 -0.38045866
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] 0.07534757 -0.11062768 -0.25384825 0.81737808 -1.12565192 0.72487247
[7] 0.63823291 -0.30708462 -0.77730292 -0.19392631 0.27645116 -1.68739637
[13] 0.47124823 0.16788624 0.79804352 -0.18207134 1.69969081 -0.12653931
[19] 0.81910839 -0.34468753 -1.24829534 -0.68243626 -0.98744283 -0.14840811
[25] 0.56240004 0.51450528 0.45500499 0.82405315 -0.61428326 0.65276217
[31] 0.57833383 0.51893407 0.14541248 -1.55217026 0.92821683 -0.03062525
[37] 0.23838969 -0.49702727 0.04197453 -2.15220526 -1.01596916 -1.15148292
[43] -0.15027994 0.15490784 -0.40574101 0.73039861 -0.27039190 -1.16236298
[49] -0.32633569 -0.79952487 -0.94876346 -0.13089435 0.43214597 -0.56818921
[55] 2.01684508 -0.82919707 0.85473125 1.64459660 1.27949264 0.35604287
[61] -0.36903214 -2.11558527 -0.92383611 -2.15486428 0.16846347 -0.69597146
[67] -0.47219250 -0.14970865 -0.07834935 -1.54346880 1.52148548 -0.11910773
[73] 0.75005270 -1.51437805 0.47413169 0.95331461 1.83751031 0.19987434
[79] 0.05371480 -0.64942769 -0.53728274 -0.21584294 -0.14085315 -0.23399484
[85] -1.69830689 -0.63909399 -0.76948296 0.32579628 -0.25839902 1.28043837
[91] -0.31170169 0.13348002 -1.46557316 0.86365946 -0.27565459 0.37554626
[97] 1.89230923 -0.34808095 1.09947815 -0.38045866
> colMin(tmp)
[1] 0.07534757 -0.11062768 -0.25384825 0.81737808 -1.12565192 0.72487247
[7] 0.63823291 -0.30708462 -0.77730292 -0.19392631 0.27645116 -1.68739637
[13] 0.47124823 0.16788624 0.79804352 -0.18207134 1.69969081 -0.12653931
[19] 0.81910839 -0.34468753 -1.24829534 -0.68243626 -0.98744283 -0.14840811
[25] 0.56240004 0.51450528 0.45500499 0.82405315 -0.61428326 0.65276217
[31] 0.57833383 0.51893407 0.14541248 -1.55217026 0.92821683 -0.03062525
[37] 0.23838969 -0.49702727 0.04197453 -2.15220526 -1.01596916 -1.15148292
[43] -0.15027994 0.15490784 -0.40574101 0.73039861 -0.27039190 -1.16236298
[49] -0.32633569 -0.79952487 -0.94876346 -0.13089435 0.43214597 -0.56818921
[55] 2.01684508 -0.82919707 0.85473125 1.64459660 1.27949264 0.35604287
[61] -0.36903214 -2.11558527 -0.92383611 -2.15486428 0.16846347 -0.69597146
[67] -0.47219250 -0.14970865 -0.07834935 -1.54346880 1.52148548 -0.11910773
[73] 0.75005270 -1.51437805 0.47413169 0.95331461 1.83751031 0.19987434
[79] 0.05371480 -0.64942769 -0.53728274 -0.21584294 -0.14085315 -0.23399484
[85] -1.69830689 -0.63909399 -0.76948296 0.32579628 -0.25839902 1.28043837
[91] -0.31170169 0.13348002 -1.46557316 0.86365946 -0.27565459 0.37554626
[97] 1.89230923 -0.34808095 1.09947815 -0.38045866
> colMedians(tmp)
[1] 0.07534757 -0.11062768 -0.25384825 0.81737808 -1.12565192 0.72487247
[7] 0.63823291 -0.30708462 -0.77730292 -0.19392631 0.27645116 -1.68739637
[13] 0.47124823 0.16788624 0.79804352 -0.18207134 1.69969081 -0.12653931
[19] 0.81910839 -0.34468753 -1.24829534 -0.68243626 -0.98744283 -0.14840811
[25] 0.56240004 0.51450528 0.45500499 0.82405315 -0.61428326 0.65276217
[31] 0.57833383 0.51893407 0.14541248 -1.55217026 0.92821683 -0.03062525
[37] 0.23838969 -0.49702727 0.04197453 -2.15220526 -1.01596916 -1.15148292
[43] -0.15027994 0.15490784 -0.40574101 0.73039861 -0.27039190 -1.16236298
[49] -0.32633569 -0.79952487 -0.94876346 -0.13089435 0.43214597 -0.56818921
[55] 2.01684508 -0.82919707 0.85473125 1.64459660 1.27949264 0.35604287
[61] -0.36903214 -2.11558527 -0.92383611 -2.15486428 0.16846347 -0.69597146
[67] -0.47219250 -0.14970865 -0.07834935 -1.54346880 1.52148548 -0.11910773
[73] 0.75005270 -1.51437805 0.47413169 0.95331461 1.83751031 0.19987434
[79] 0.05371480 -0.64942769 -0.53728274 -0.21584294 -0.14085315 -0.23399484
[85] -1.69830689 -0.63909399 -0.76948296 0.32579628 -0.25839902 1.28043837
[91] -0.31170169 0.13348002 -1.46557316 0.86365946 -0.27565459 0.37554626
[97] 1.89230923 -0.34808095 1.09947815 -0.38045866
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.07534757 -0.1106277 -0.2538482 0.8173781 -1.125652 0.7248725 0.6382329
[2,] 0.07534757 -0.1106277 -0.2538482 0.8173781 -1.125652 0.7248725 0.6382329
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.3070846 -0.7773029 -0.1939263 0.2764512 -1.687396 0.4712482 0.1678862
[2,] -0.3070846 -0.7773029 -0.1939263 0.2764512 -1.687396 0.4712482 0.1678862
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 0.7980435 -0.1820713 1.699691 -0.1265393 0.8191084 -0.3446875 -1.248295
[2,] 0.7980435 -0.1820713 1.699691 -0.1265393 0.8191084 -0.3446875 -1.248295
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.6824363 -0.9874428 -0.1484081 0.5624 0.5145053 0.455005 0.8240532
[2,] -0.6824363 -0.9874428 -0.1484081 0.5624 0.5145053 0.455005 0.8240532
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -0.6142833 0.6527622 0.5783338 0.5189341 0.1454125 -1.55217 0.9282168
[2,] -0.6142833 0.6527622 0.5783338 0.5189341 0.1454125 -1.55217 0.9282168
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -0.03062525 0.2383897 -0.4970273 0.04197453 -2.152205 -1.015969 -1.151483
[2,] -0.03062525 0.2383897 -0.4970273 0.04197453 -2.152205 -1.015969 -1.151483
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.1502799 0.1549078 -0.405741 0.7303986 -0.2703919 -1.162363 -0.3263357
[2,] -0.1502799 0.1549078 -0.405741 0.7303986 -0.2703919 -1.162363 -0.3263357
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -0.7995249 -0.9487635 -0.1308944 0.432146 -0.5681892 2.016845 -0.8291971
[2,] -0.7995249 -0.9487635 -0.1308944 0.432146 -0.5681892 2.016845 -0.8291971
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.8547313 1.644597 1.279493 0.3560429 -0.3690321 -2.115585 -0.9238361
[2,] 0.8547313 1.644597 1.279493 0.3560429 -0.3690321 -2.115585 -0.9238361
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -2.154864 0.1684635 -0.6959715 -0.4721925 -0.1497086 -0.07834935 -1.543469
[2,] -2.154864 0.1684635 -0.6959715 -0.4721925 -0.1497086 -0.07834935 -1.543469
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 1.521485 -0.1191077 0.7500527 -1.514378 0.4741317 0.9533146 1.83751
[2,] 1.521485 -0.1191077 0.7500527 -1.514378 0.4741317 0.9533146 1.83751
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 0.1998743 0.0537148 -0.6494277 -0.5372827 -0.2158429 -0.1408531 -0.2339948
[2,] 0.1998743 0.0537148 -0.6494277 -0.5372827 -0.2158429 -0.1408531 -0.2339948
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -1.698307 -0.639094 -0.769483 0.3257963 -0.258399 1.280438 -0.3117017
[2,] -1.698307 -0.639094 -0.769483 0.3257963 -0.258399 1.280438 -0.3117017
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 0.13348 -1.465573 0.8636595 -0.2756546 0.3755463 1.892309 -0.348081
[2,] 0.13348 -1.465573 0.8636595 -0.2756546 0.3755463 1.892309 -0.348081
[,99] [,100]
[1,] 1.099478 -0.3804587
[2,] 1.099478 -0.3804587
>
>
> Max(tmp2)
[1] 2.864222
> Min(tmp2)
[1] -2.358019
> mean(tmp2)
[1] -0.03287578
> Sum(tmp2)
[1] -3.287578
> Var(tmp2)
[1] 0.9382279
>
> rowMeans(tmp2)
[1] -1.49809661 -0.12035742 -0.59980597 0.73133225 -0.75608555 -0.72519826
[7] 0.13559340 2.14633066 0.67086762 0.21938878 -0.53839960 -0.32847232
[13] -1.16684386 -1.55986656 -0.40126966 0.52165904 -0.48326333 0.61822699
[19] 2.86422189 -0.03788624 0.78114795 -0.49689596 -2.35801920 -0.83896409
[25] -0.84433203 0.96873235 -1.80871053 -0.77432806 -1.38324468 -0.51667436
[31] 0.47430444 -1.68866969 0.26994600 -1.15327233 -0.43022369 0.92504764
[37] 1.22725294 1.73327979 0.03288979 0.13897043 -0.72580804 1.72942833
[43] -0.73090635 0.40600212 0.55693334 -0.56738316 -0.38534787 0.43336680
[49] -0.73219865 0.94220137 0.32799355 0.48788542 -1.06692564 -1.11508067
[55] 0.69768107 0.44194597 -0.39578552 0.06949378 0.58041903 0.60468718
[61] -0.24516633 0.56829568 -0.50172596 -0.07952232 -0.88394278 -0.07275446
[67] -0.94010580 0.35489149 -0.77861937 -0.72219384 -0.30613545 1.44495163
[73] 0.11212757 0.41355252 -1.38264877 -0.17131239 0.58783163 1.65958785
[79] 2.26687134 0.52567933 -0.67202468 -0.38692740 0.90025969 0.28400822
[85] -0.29575545 0.23614044 0.39909610 -0.01388380 0.73204281 -0.26856527
[91] -2.34594619 -0.18178868 -0.03817704 -2.17754556 0.09370159 -0.27858131
[97] 0.59467638 -0.26309032 1.18153805 1.85466902
> rowSums(tmp2)
[1] -1.49809661 -0.12035742 -0.59980597 0.73133225 -0.75608555 -0.72519826
[7] 0.13559340 2.14633066 0.67086762 0.21938878 -0.53839960 -0.32847232
[13] -1.16684386 -1.55986656 -0.40126966 0.52165904 -0.48326333 0.61822699
[19] 2.86422189 -0.03788624 0.78114795 -0.49689596 -2.35801920 -0.83896409
[25] -0.84433203 0.96873235 -1.80871053 -0.77432806 -1.38324468 -0.51667436
[31] 0.47430444 -1.68866969 0.26994600 -1.15327233 -0.43022369 0.92504764
[37] 1.22725294 1.73327979 0.03288979 0.13897043 -0.72580804 1.72942833
[43] -0.73090635 0.40600212 0.55693334 -0.56738316 -0.38534787 0.43336680
[49] -0.73219865 0.94220137 0.32799355 0.48788542 -1.06692564 -1.11508067
[55] 0.69768107 0.44194597 -0.39578552 0.06949378 0.58041903 0.60468718
[61] -0.24516633 0.56829568 -0.50172596 -0.07952232 -0.88394278 -0.07275446
[67] -0.94010580 0.35489149 -0.77861937 -0.72219384 -0.30613545 1.44495163
[73] 0.11212757 0.41355252 -1.38264877 -0.17131239 0.58783163 1.65958785
[79] 2.26687134 0.52567933 -0.67202468 -0.38692740 0.90025969 0.28400822
[85] -0.29575545 0.23614044 0.39909610 -0.01388380 0.73204281 -0.26856527
[91] -2.34594619 -0.18178868 -0.03817704 -2.17754556 0.09370159 -0.27858131
[97] 0.59467638 -0.26309032 1.18153805 1.85466902
> 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] -1.49809661 -0.12035742 -0.59980597 0.73133225 -0.75608555 -0.72519826
[7] 0.13559340 2.14633066 0.67086762 0.21938878 -0.53839960 -0.32847232
[13] -1.16684386 -1.55986656 -0.40126966 0.52165904 -0.48326333 0.61822699
[19] 2.86422189 -0.03788624 0.78114795 -0.49689596 -2.35801920 -0.83896409
[25] -0.84433203 0.96873235 -1.80871053 -0.77432806 -1.38324468 -0.51667436
[31] 0.47430444 -1.68866969 0.26994600 -1.15327233 -0.43022369 0.92504764
[37] 1.22725294 1.73327979 0.03288979 0.13897043 -0.72580804 1.72942833
[43] -0.73090635 0.40600212 0.55693334 -0.56738316 -0.38534787 0.43336680
[49] -0.73219865 0.94220137 0.32799355 0.48788542 -1.06692564 -1.11508067
[55] 0.69768107 0.44194597 -0.39578552 0.06949378 0.58041903 0.60468718
[61] -0.24516633 0.56829568 -0.50172596 -0.07952232 -0.88394278 -0.07275446
[67] -0.94010580 0.35489149 -0.77861937 -0.72219384 -0.30613545 1.44495163
[73] 0.11212757 0.41355252 -1.38264877 -0.17131239 0.58783163 1.65958785
[79] 2.26687134 0.52567933 -0.67202468 -0.38692740 0.90025969 0.28400822
[85] -0.29575545 0.23614044 0.39909610 -0.01388380 0.73204281 -0.26856527
[91] -2.34594619 -0.18178868 -0.03817704 -2.17754556 0.09370159 -0.27858131
[97] 0.59467638 -0.26309032 1.18153805 1.85466902
> rowMin(tmp2)
[1] -1.49809661 -0.12035742 -0.59980597 0.73133225 -0.75608555 -0.72519826
[7] 0.13559340 2.14633066 0.67086762 0.21938878 -0.53839960 -0.32847232
[13] -1.16684386 -1.55986656 -0.40126966 0.52165904 -0.48326333 0.61822699
[19] 2.86422189 -0.03788624 0.78114795 -0.49689596 -2.35801920 -0.83896409
[25] -0.84433203 0.96873235 -1.80871053 -0.77432806 -1.38324468 -0.51667436
[31] 0.47430444 -1.68866969 0.26994600 -1.15327233 -0.43022369 0.92504764
[37] 1.22725294 1.73327979 0.03288979 0.13897043 -0.72580804 1.72942833
[43] -0.73090635 0.40600212 0.55693334 -0.56738316 -0.38534787 0.43336680
[49] -0.73219865 0.94220137 0.32799355 0.48788542 -1.06692564 -1.11508067
[55] 0.69768107 0.44194597 -0.39578552 0.06949378 0.58041903 0.60468718
[61] -0.24516633 0.56829568 -0.50172596 -0.07952232 -0.88394278 -0.07275446
[67] -0.94010580 0.35489149 -0.77861937 -0.72219384 -0.30613545 1.44495163
[73] 0.11212757 0.41355252 -1.38264877 -0.17131239 0.58783163 1.65958785
[79] 2.26687134 0.52567933 -0.67202468 -0.38692740 0.90025969 0.28400822
[85] -0.29575545 0.23614044 0.39909610 -0.01388380 0.73204281 -0.26856527
[91] -2.34594619 -0.18178868 -0.03817704 -2.17754556 0.09370159 -0.27858131
[97] 0.59467638 -0.26309032 1.18153805 1.85466902
>
> colMeans(tmp2)
[1] -0.03287578
> colSums(tmp2)
[1] -3.287578
> colVars(tmp2)
[1] 0.9382279
> colSd(tmp2)
[1] 0.9686216
> colMax(tmp2)
[1] 2.864222
> colMin(tmp2)
[1] -2.358019
> colMedians(tmp2)
[1] -0.05546575
> colRanges(tmp2)
[,1]
[1,] -2.358019
[2,] 2.864222
>
> 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] -3.64824349 -1.88093816 1.21601178 2.50083657 3.42605264 -0.63429997
[7] 0.01474606 0.66111938 -7.56476733 4.18575860
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.7512594
[2,] -1.0908119
[3,] -0.5171811
[4,] 0.3551628
[5,] 1.3032151
>
> rowApply(tmp,sum)
[1] 2.5426256 -1.1083067 0.3015304 0.2374746 -2.3029850 -3.2255095
[7] 4.6874245 -2.8558892 -1.8746594 1.8745710
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 4 5 9 8 3 3 4 3 1 1
[2,] 3 9 3 9 5 4 2 8 3 2
[3,] 1 2 10 1 10 10 3 7 7 5
[4,] 8 6 4 4 1 9 5 9 5 10
[5,] 10 8 5 5 6 8 9 5 6 9
[6,] 7 4 7 3 4 2 7 4 10 3
[7,] 5 7 2 7 9 7 8 1 9 6
[8,] 9 1 1 6 2 6 10 10 8 8
[9,] 2 3 6 2 8 1 1 2 2 7
[10,] 6 10 8 10 7 5 6 6 4 4
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -1.642351013 4.021816165 -2.225233759 1.014801717 2.833163012
[6] 1.615620282 3.246291749 3.168310690 -2.949095687 2.408616452
[11] -1.172805381 4.180699666 -3.419957932 2.288836715 -0.047927726
[16] 0.032048012 -0.009696865 -2.373277594 0.565666841 3.027119422
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.53305147
[2,] -0.56571816
[3,] -0.52737741
[4,] 0.08656287
[5,] 0.89723317
>
> rowApply(tmp,sum)
[1] 6.6886383 1.2342646 -0.7402035 0.8088169 6.5711284
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 4 7 3 16 12
[2,] 13 19 18 13 3
[3,] 3 13 7 3 11
[4,] 16 18 1 12 15
[5,] 19 12 6 18 10
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.56571816 0.7243015 -0.68155785 0.8943377 2.048921719 -0.2740790
[2,] -0.52737741 2.5538108 0.16838064 1.1457169 0.117384240 0.6844253
[3,] -1.53305147 1.2983329 -0.60131120 -2.2611002 -0.620299049 0.9856745
[4,] 0.89723317 0.1875925 -1.15599676 0.1562011 1.296275417 1.5907757
[5,] 0.08656287 -0.7422215 0.04525141 1.0796461 -0.009119316 -1.3711763
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.99432685 0.8689216 -2.06915468 -0.3509654 0.3444014 0.7292549
[2,] -0.86678110 2.8062156 -0.03050485 -0.3560999 0.6175077 0.3268111
[3,] 0.91906050 0.7236308 0.07930734 0.8934033 -2.0506527 0.2679229
[4,] 0.01899569 -0.5537763 -0.72076216 0.0178321 -1.3789855 2.2670756
[5,] 2.18068980 -0.6766810 -0.20798134 2.2044463 1.2949237 0.5896351
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.9428099 1.0955735 -0.1933237 -0.1605984 -0.05613488 0.7087054
[2,] -1.2208174 0.3630155 -0.7803596 -0.3816982 -1.10790728 -1.6316658
[3,] -0.5117066 0.2679232 1.8562710 -0.5529202 -0.93975367 0.5435658
[4,] -0.4718753 1.1845739 -0.8839908 0.3120683 0.67165111 -1.2304852
[5,] -0.2727487 -0.6222494 -0.0465247 0.8151964 1.42244786 -0.7633979
[,19] [,20]
[1,] 0.6230228 2.95121271
[2,] -0.6129647 -0.03282705
[3,] 1.7470001 -1.25150079
[4,] -0.5863585 -0.80922735
[5,] -0.6050328 2.16946190
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-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-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 648 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 562 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-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 -1.073889 0.691749 2.165633 0.5899644 -1.212063 -0.532394 -0.1093589
col8 col9 col10 col11 col12 col13 col14
row1 1.170258 0.8563776 -0.1693227 1.168014 1.893176 0.1027869 -1.345692
col15 col16 col17 col18 col19 col20
row1 -0.3896698 1.509088 0.004220441 0.5828658 0.8385369 -0.9599046
> tmp[,"col10"]
col10
row1 -0.1693227
row2 -1.1855229
row3 -0.2344207
row4 1.3398009
row5 0.1699585
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 -1.0738885 0.691749 2.1656332 0.5899644 -1.2120632 -0.5323940
row5 -0.8169617 -1.856841 -0.5842451 0.7466740 -0.3601679 0.5345771
col7 col8 col9 col10 col11 col12
row1 -0.10935894 1.1702584 0.8563776 -0.1693227 1.1680138 1.8931758
row5 -0.08660928 -0.3319652 -0.7182824 0.1699585 -0.5623554 0.8193051
col13 col14 col15 col16 col17 col18
row1 0.1027869 -1.3456924 -0.3896698 1.5090884 0.004220441 0.5828658
row5 0.1191387 -0.3049317 -0.2110267 -0.2877401 1.468537500 1.8608722
col19 col20
row1 0.8385369 -0.9599046
row5 -1.4729275 -0.1945880
> tmp[,c("col6","col20")]
col6 col20
row1 -0.5323940 -0.9599046
row2 -1.1472812 -0.9835416
row3 1.7353523 0.6492768
row4 -0.1425281 1.6899616
row5 0.5345771 -0.1945880
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.5323940 -0.9599046
row5 0.5345771 -0.1945880
>
>
>
>
> 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 51.03203 49.72651 48.34079 50.64211 51.67104 105.0219 50.32284 49.41479
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.47488 48.91805 50.81811 51.70026 48.37379 50.55231 50.44247 49.84844
col17 col18 col19 col20
row1 49.49588 49.20534 50.42777 103.5805
> tmp[,"col10"]
col10
row1 48.91805
row2 31.19129
row3 31.19948
row4 30.23364
row5 50.93284
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 51.03203 49.72651 48.34079 50.64211 51.67104 105.0219 50.32284 49.41479
row5 47.01953 50.99273 50.34509 52.91169 50.78409 104.1666 50.16279 49.09439
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.47488 48.91805 50.81811 51.70026 48.37379 50.55231 50.44247 49.84844
row5 50.05638 50.93284 50.62993 49.96563 50.25704 51.12580 49.60001 50.00417
col17 col18 col19 col20
row1 49.49588 49.20534 50.42777 103.5805
row5 49.87317 49.40914 49.98731 104.3289
> tmp[,c("col6","col20")]
col6 col20
row1 105.02194 103.58049
row2 74.41069 76.48115
row3 72.63960 75.90645
row4 74.61493 74.43315
row5 104.16665 104.32890
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.0219 103.5805
row5 104.1666 104.3289
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.0219 103.5805
row5 104.1666 104.3289
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 1.7724162
[2,] -0.7875699
[3,] 0.3944640
[4,] 0.4764739
[5,] 1.5834252
> tmp[,c("col17","col7")]
col17 col7
[1,] -1.8669721 0.3050475
[2,] 0.2346447 -0.2641803
[3,] -0.2859930 -2.1711408
[4,] 1.1919039 0.2377203
[5,] 1.3760991 -0.8854988
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 0.7137276 1.8050795
[2,] 0.4822610 -0.8558816
[3,] 1.0324212 1.4519454
[4,] -1.0966919 -1.7725250
[5,] 0.2339739 -0.1422817
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 0.7137276
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 0.7137276
[2,] 0.4822610
>
>
>
> 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 1.4779793 -0.6847213 -0.828244 0.3601158 -1.301784 1.3336943 1.0049660
row1 -0.1819628 -2.7033680 -1.300480 -0.5050594 -1.387780 0.2559511 -0.5314923
[,8] [,9] [,10] [,11] [,12] [,13]
row3 0.2081165 0.4109449 -0.18530528 1.316849 0.05638342 -1.9090360
row1 -0.9515518 0.5649739 -0.01226892 0.200581 -1.67586711 0.5755895
[,14] [,15] [,16] [,17] [,18] [,19]
row3 -1.6142284 0.8777118 -0.06853644 -0.3241232 -0.3303484 -2.189586
row1 -0.9034715 0.4757976 -0.14066797 -1.9780251 -1.3926654 -1.051213
[,20]
row3 -1.9680920
row1 0.5166566
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.8129249 -0.2854082 -1.259691 1.404597 0.1683988 1.697922 -0.5451834
[,8] [,9] [,10]
row2 0.8248264 -0.3041702 1.972304
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -0.2479684 -0.9813747 0.2465047 -0.9778858 0.03892591 1.429801 1.639026
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 1.113787 0.6833699 0.2849576 -0.7424731 0.4085967 0.04701079 -0.7417351
[,15] [,16] [,17] [,18] [,19] [,20]
row5 0.4654594 1.340949 -0.2140786 0.435357 0.5572172 -0.6657479
>
>
> 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: 0x6116c1746a90>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM67c387c99b213"
[2] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM67c3821c3de41"
[3] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM67c384e3e99d7"
[4] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM67c383a8926b8"
[5] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM67c38be29279"
[6] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM67c383dfcc96a"
[7] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM67c3851b4765c"
[8] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM67c385ee781da"
[9] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM67c38d077d05"
[10] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM67c3873c98057"
[11] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM67c387528eeaf"
[12] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM67c381c26d5ed"
[13] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM67c38508ea3fe"
[14] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM67c3820a5dc20"
[15] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM67c384e04fa09"
>
>
> ### 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: 0x6116c3297860>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x6116c3297860>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x6116c3297860>
> rowMedians(tmp)
[1] 0.218617891 -0.416229838 -0.503608157 -0.373440759 0.192904416
[6] -0.075874731 0.321566334 -0.092707900 -0.364154491 -0.031068360
[11] 0.223921117 -0.187549082 -0.293793015 0.344128994 -0.388951528
[16] 0.269972151 0.061439141 0.117251901 -0.303039809 -0.347068920
[21] 0.287501231 -0.361085981 0.411737508 0.022844440 0.296318062
[26] -0.315061554 0.112656708 -0.498915678 -0.084229804 -0.113991247
[31] 0.193808935 0.285994378 -0.060319428 -0.081544136 0.264124644
[36] -0.223317637 0.247253179 0.098651083 0.443353778 0.112159534
[41] -0.583310470 -0.382122900 -0.111454697 -0.018879248 -0.272026611
[46] -0.002135320 -0.330193840 0.203049016 0.160248034 -0.392110898
[51] 0.467630302 -0.007204854 -0.251092709 0.170430016 -0.435481676
[56] 0.689420901 0.325211835 0.489553466 -0.176161953 0.458718959
[61] -0.048385398 0.345099530 -0.098042751 -0.654307724 -0.404321371
[66] 0.509194859 -0.240583170 0.491250386 0.287472598 0.032804921
[71] 0.074611159 0.298115827 -0.404008341 0.289749838 0.278794792
[76] 0.146419003 -0.103453516 0.437148712 0.090721733 -0.051615408
[81] -0.057467958 0.269999486 0.263851187 -0.196619735 -0.116538273
[86] -0.124171814 -0.262984211 -0.376527165 -0.363594139 0.526583697
[91] -0.115626693 0.716120264 0.083386339 -0.173104246 -0.285051863
[96] -0.579447377 -0.671394763 0.037455615 -0.009201505 -0.324369191
[101] -0.346341892 0.296654918 0.005462157 -0.042542205 0.193925107
[106] -0.292687772 0.140181083 0.545635729 -0.239905630 -0.021195270
[111] -0.502718160 -0.130332111 0.223754477 -0.370120902 0.068459282
[116] 0.046276818 -0.354415304 -0.027981894 0.011812329 -0.197559699
[121] -0.569193987 -0.104749273 -0.441868091 -0.131460677 0.078338669
[126] 0.083496066 0.054780519 -0.190587467 -0.054502018 0.308772180
[131] 0.041314565 -0.142957252 -0.079345752 0.007766074 -0.188990814
[136] -0.018764986 -0.338004853 -0.036200474 0.312530676 -0.009698147
[141] 0.030434930 0.046595792 -0.024717115 -0.383568581 0.349469618
[146] -0.022034469 0.392530809 -0.082055177 -0.434019559 0.118727821
[151] 0.168406481 -0.271208854 -0.360830559 0.234227851 0.476199896
[156] 0.211681432 -0.196737871 0.231556600 0.477533846 -0.808808088
[161] 0.466582735 0.541723383 -0.255860302 0.324085186 -0.260987986
[166] -0.293806494 -0.520862681 0.314655271 0.264019569 -0.016153818
[171] 0.773449794 0.268017246 -0.297542320 0.302560339 -0.125337144
[176] 0.124275299 0.757496183 0.339563041 0.058802745 -0.204334036
[181] -0.327233517 -0.093912180 0.269069556 0.365931680 0.307413969
[186] -0.559313077 0.168901325 -0.017708817 -0.044136635 0.057175821
[191] 0.416815686 -0.414801433 0.074760769 -0.099050244 -0.309960636
[196] 0.130874607 -0.464380521 0.217029840 0.485673247 -0.251335534
[201] -0.080716186 -0.112928391 0.654565564 0.206028051 -0.055292673
[206] -0.064827409 0.317166544 -0.311306834 -0.152981840 -0.505496123
[211] -0.135264488 0.622718009 -0.440882960 -0.791477939 0.468451093
[216] 0.098183503 0.071853033 -0.293070768 0.240522566 -0.074463591
[221] 0.145059843 -0.693390396 -0.637148257 0.075218807 -0.180308129
[226] 0.485745610 0.200373179 0.188269115 -0.349325858 -0.391420131
>
> proc.time()
user system elapsed
1.389 1.467 2.845
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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: 0x5dc33eabec10>
> .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: 0x5dc33eabec10>
> .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: 0x5dc33eabec10>
> .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: 0x5dc33eabec10>
> 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: 0x5dc33f7812d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5dc33f7812d0>
> .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: 0x5dc33f7812d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5dc33f7812d0>
> .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: 0x5dc33f7812d0>
> 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: 0x5dc33fe56d70>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5dc33fe56d70>
> .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: 0x5dc33fe56d70>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5dc33fe56d70>
> .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: 0x5dc33fe56d70>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x5dc33fe56d70>
> .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: 0x5dc33fe56d70>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x5dc33fe56d70>
> .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: 0x5dc33fe56d70>
> 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: 0x5dc33f9ca370>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x5dc33f9ca370>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5dc33f9ca370>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5dc33f9ca370>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile67d516744b188" "BufferedMatrixFile67d517b11ac42"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile67d516744b188" "BufferedMatrixFile67d517b11ac42"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5dc33f915ff0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5dc33f915ff0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5dc33f915ff0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5dc33f915ff0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x5dc33f915ff0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x5dc33f915ff0>
> .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: 0x5dc33faf83d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5dc33faf83d0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5dc33faf83d0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x5dc33faf83d0>
> 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: 0x5dc3412a9fb0>
> .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: 0x5dc3412a9fb0>
> rm(P)
>
> proc.time()
user system elapsed
0.236 0.062 0.287
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
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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
0.243 0.051 0.283