Ben Bolstad
| Snapshot Date: 2025-11-06 13:40 -0500 (Thu, 06 Nov 2025) |
| 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 2025-11-07 11:32 -0500 (Fri, 07 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4818 |
| 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 251/2323 | 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 | | ||||||||
|
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: 2025-11-06 21:29:53 -0500 (Thu, 06 Nov 2025) |
| EndedAt: 2025-11-06 21:30:18 -0500 (Thu, 06 Nov 2025) |
| 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) (2025-10-20 r88955)
* 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) (2025-10-20 r88955) -- "Unsuffered Consequences"
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
0.242 0.052 0.282
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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-3.23-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 478818 25.6 1048392 56 639317 34.2
Vcells 885623 6.8 8388608 64 2082728 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 Nov 6 21:30:08 2025"
> 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 Nov 6 21:30:08 2025"
>
>
> 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: 0x5a6b8ff3f5e0>
>
>
>
> 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 Nov 6 21:30:08 2025"
> 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 Nov 6 21:30:09 2025"
>
> ColMode(tmp2)
<pointer: 0x5a6b8ff3f5e0>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 101.19842130 1.9656180 0.2804712 -1.5054818
[2,] -0.85211785 -1.6670182 -2.3831010 -0.2598899
[3,] 0.38996480 -0.9039762 -2.1044676 1.3041529
[4,] -0.06574826 -2.5427235 -0.8815883 -0.6672668
> 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 : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 101.19842130 1.9656180 0.2804712 1.5054818
[2,] 0.85211785 1.6670182 2.3831010 0.2598899
[3,] 0.38996480 0.9039762 2.1044676 1.3041529
[4,] 0.06574826 2.5427235 0.8815883 0.6672668
> 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 : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 10.0597426 1.4020050 0.5295953 1.226981
[2,] 0.9231023 1.2911306 1.5437296 0.509794
[3,] 0.6244716 0.9507767 1.4506783 1.141995
[4,] 0.2564142 1.5945920 0.9389293 0.816864
>
> 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 : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 226.79585 40.98567 30.57642 38.77529
[2,] 35.08314 39.57832 42.82040 30.35783
[3,] 31.63468 35.41174 41.61125 37.72410
[4,] 27.62989 43.48864 35.27088 33.83591
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x5a6b8faca840>
> exp(tmp5)
<pointer: 0x5a6b8faca840>
> log(tmp5,2)
<pointer: 0x5a6b8faca840>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 472.0458
> Min(tmp5)
[1] 53.33634
> mean(tmp5)
[1] 73.40133
> Sum(tmp5)
[1] 14680.27
> Var(tmp5)
[1] 876.4736
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 92.43153 74.31906 73.13453 70.57114 72.44366 68.92066 72.21396 70.95913
[9] 68.22014 70.79945
> rowSums(tmp5)
[1] 1848.631 1486.381 1462.691 1411.423 1448.873 1378.413 1444.279 1419.183
[9] 1364.403 1415.989
> rowVars(tmp5)
[1] 8063.70317 60.69213 71.42039 65.18901 114.02887 113.11030
[7] 77.34381 46.45754 50.91516 61.20113
> rowSd(tmp5)
[1] 89.798125 7.790515 8.451058 8.073971 10.678430 10.635333 8.794533
[8] 6.815977 7.135486 7.823115
> rowMax(tmp5)
[1] 472.04584 89.12505 89.45997 90.51591 90.14796 90.89639 85.11505
[8] 82.24441 88.00765 84.17458
> rowMin(tmp5)
[1] 55.09748 57.63615 56.07722 57.50800 54.39415 53.33634 55.07771 59.29439
[9] 59.02306 57.77993
>
> colMeans(tmp5)
[1] 109.79233 80.19766 75.38124 67.48796 67.96997 73.23994 72.70456
[8] 70.72687 72.22137 68.05200 74.79970 74.64123 72.23758 75.68219
[15] 71.15059 68.93408 66.07931 65.90168 70.23732 70.58893
> colSums(tmp5)
[1] 1097.9233 801.9766 753.8124 674.8796 679.6997 732.3994 727.0456
[8] 707.2687 722.2137 680.5200 747.9970 746.4123 722.3758 756.8219
[15] 711.5059 689.3408 660.7931 659.0168 702.3732 705.8893
> colVars(tmp5)
[1] 16248.62800 38.11963 90.75111 60.00062 125.72747 50.56913
[7] 34.98653 56.45815 78.95058 38.81602 143.12267 62.70541
[13] 122.26823 24.81738 92.51754 43.61821 15.27577 125.20314
[19] 57.97629 47.73423
> colSd(tmp5)
[1] 127.470106 6.174110 9.526338 7.746007 11.212826 7.111198
[7] 5.914942 7.513864 8.885414 6.230250 11.963389 7.918675
[13] 11.057497 4.981705 9.618604 6.604408 3.908422 11.189421
[19] 7.614217 6.908996
> colMax(tmp5)
[1] 472.04584 90.51591 89.12505 80.70568 89.45997 84.59577 82.24441
[8] 80.78677 84.17458 81.58963 90.14796 86.70422 87.86024 82.51301
[15] 90.89639 75.04715 71.61557 86.04481 77.03308 79.74335
> colMin(tmp5)
[1] 57.50800 71.72404 63.07802 57.77993 55.09748 64.96003 62.57401 58.92131
[9] 58.23380 61.42467 53.33634 63.88742 56.71180 68.34511 61.55976 56.09870
[17] 59.39199 53.40112 55.55256 57.63615
>
>
> ### 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] 92.43153 74.31906 73.13453 70.57114 72.44366 68.92066 72.21396 NA
[9] 68.22014 70.79945
> rowSums(tmp5)
[1] 1848.631 1486.381 1462.691 1411.423 1448.873 1378.413 1444.279 NA
[9] 1364.403 1415.989
> rowVars(tmp5)
[1] 8063.70317 60.69213 71.42039 65.18901 114.02887 113.11030
[7] 77.34381 49.03467 50.91516 61.20113
> rowSd(tmp5)
[1] 89.798125 7.790515 8.451058 8.073971 10.678430 10.635333 8.794533
[8] 7.002476 7.135486 7.823115
> rowMax(tmp5)
[1] 472.04584 89.12505 89.45997 90.51591 90.14796 90.89639 85.11505
[8] NA 88.00765 84.17458
> rowMin(tmp5)
[1] 55.09748 57.63615 56.07722 57.50800 54.39415 53.33634 55.07771 NA
[9] 59.02306 57.77993
>
> colMeans(tmp5)
[1] 109.79233 80.19766 75.38124 NA 67.96997 73.23994 72.70456
[8] 70.72687 72.22137 68.05200 74.79970 74.64123 72.23758 75.68219
[15] 71.15059 68.93408 66.07931 65.90168 70.23732 70.58893
> colSums(tmp5)
[1] 1097.9233 801.9766 753.8124 NA 679.6997 732.3994 727.0456
[8] 707.2687 722.2137 680.5200 747.9970 746.4123 722.3758 756.8219
[15] 711.5059 689.3408 660.7931 659.0168 702.3732 705.8893
> colVars(tmp5)
[1] 16248.62800 38.11963 90.75111 NA 125.72747 50.56913
[7] 34.98653 56.45815 78.95058 38.81602 143.12267 62.70541
[13] 122.26823 24.81738 92.51754 43.61821 15.27577 125.20314
[19] 57.97629 47.73423
> colSd(tmp5)
[1] 127.470106 6.174110 9.526338 NA 11.212826 7.111198
[7] 5.914942 7.513864 8.885414 6.230250 11.963389 7.918675
[13] 11.057497 4.981705 9.618604 6.604408 3.908422 11.189421
[19] 7.614217 6.908996
> colMax(tmp5)
[1] 472.04584 90.51591 89.12505 NA 89.45997 84.59577 82.24441
[8] 80.78677 84.17458 81.58963 90.14796 86.70422 87.86024 82.51301
[15] 90.89639 75.04715 71.61557 86.04481 77.03308 79.74335
> colMin(tmp5)
[1] 57.50800 71.72404 63.07802 NA 55.09748 64.96003 62.57401 58.92131
[9] 58.23380 61.42467 53.33634 63.88742 56.71180 68.34511 61.55976 56.09870
[17] 59.39199 53.40112 55.55256 57.63615
>
> Max(tmp5,na.rm=TRUE)
[1] 472.0458
> Min(tmp5,na.rm=TRUE)
[1] 53.33634
> mean(tmp5,na.rm=TRUE)
[1] 73.41231
> Sum(tmp5,na.rm=TRUE)
[1] 14609.05
> Var(tmp5,na.rm=TRUE)
[1] 880.876
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.43153 74.31906 73.13453 70.57114 72.44366 68.92066 72.21396 70.94565
[9] 68.22014 70.79945
> rowSums(tmp5,na.rm=TRUE)
[1] 1848.631 1486.381 1462.691 1411.423 1448.873 1378.413 1444.279 1347.967
[9] 1364.403 1415.989
> rowVars(tmp5,na.rm=TRUE)
[1] 8063.70317 60.69213 71.42039 65.18901 114.02887 113.11030
[7] 77.34381 49.03467 50.91516 61.20113
> rowSd(tmp5,na.rm=TRUE)
[1] 89.798125 7.790515 8.451058 8.073971 10.678430 10.635333 8.794533
[8] 7.002476 7.135486 7.823115
> rowMax(tmp5,na.rm=TRUE)
[1] 472.04584 89.12505 89.45997 90.51591 90.14796 90.89639 85.11505
[8] 82.24441 88.00765 84.17458
> rowMin(tmp5,na.rm=TRUE)
[1] 55.09748 57.63615 56.07722 57.50800 54.39415 53.33634 55.07771 59.29439
[9] 59.02306 57.77993
>
> colMeans(tmp5,na.rm=TRUE)
[1] 109.79233 80.19766 75.38124 67.07380 67.96997 73.23994 72.70456
[8] 70.72687 72.22137 68.05200 74.79970 74.64123 72.23758 75.68219
[15] 71.15059 68.93408 66.07931 65.90168 70.23732 70.58893
> colSums(tmp5,na.rm=TRUE)
[1] 1097.9233 801.9766 753.8124 603.6642 679.6997 732.3994 727.0456
[8] 707.2687 722.2137 680.5200 747.9970 746.4123 722.3758 756.8219
[15] 711.5059 689.3408 660.7931 659.0168 702.3732 705.8893
> colVars(tmp5,na.rm=TRUE)
[1] 16248.62800 38.11963 90.75111 65.57108 125.72747 50.56913
[7] 34.98653 56.45815 78.95058 38.81602 143.12267 62.70541
[13] 122.26823 24.81738 92.51754 43.61821 15.27577 125.20314
[19] 57.97629 47.73423
> colSd(tmp5,na.rm=TRUE)
[1] 127.470106 6.174110 9.526338 8.097597 11.212826 7.111198
[7] 5.914942 7.513864 8.885414 6.230250 11.963389 7.918675
[13] 11.057497 4.981705 9.618604 6.604408 3.908422 11.189421
[19] 7.614217 6.908996
> colMax(tmp5,na.rm=TRUE)
[1] 472.04584 90.51591 89.12505 80.70568 89.45997 84.59577 82.24441
[8] 80.78677 84.17458 81.58963 90.14796 86.70422 87.86024 82.51301
[15] 90.89639 75.04715 71.61557 86.04481 77.03308 79.74335
> colMin(tmp5,na.rm=TRUE)
[1] 57.50800 71.72404 63.07802 57.77993 55.09748 64.96003 62.57401 58.92131
[9] 58.23380 61.42467 53.33634 63.88742 56.71180 68.34511 61.55976 56.09870
[17] 59.39199 53.40112 55.55256 57.63615
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.43153 74.31906 73.13453 70.57114 72.44366 68.92066 72.21396 NaN
[9] 68.22014 70.79945
> rowSums(tmp5,na.rm=TRUE)
[1] 1848.631 1486.381 1462.691 1411.423 1448.873 1378.413 1444.279 0.000
[9] 1364.403 1415.989
> rowVars(tmp5,na.rm=TRUE)
[1] 8063.70317 60.69213 71.42039 65.18901 114.02887 113.11030
[7] 77.34381 NA 50.91516 61.20113
> rowSd(tmp5,na.rm=TRUE)
[1] 89.798125 7.790515 8.451058 8.073971 10.678430 10.635333 8.794533
[8] NA 7.135486 7.823115
> rowMax(tmp5,na.rm=TRUE)
[1] 472.04584 89.12505 89.45997 90.51591 90.14796 90.89639 85.11505
[8] NA 88.00765 84.17458
> rowMin(tmp5,na.rm=TRUE)
[1] 55.09748 57.63615 56.07722 57.50800 54.39415 53.33634 55.07771 NA
[9] 59.02306 57.77993
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 113.34317 81.13918 75.12472 NaN 68.93393 73.31737 71.64457
[8] 71.23951 71.25000 68.78837 74.71982 75.83609 72.79747 75.33268
[15] 71.93302 68.41365 65.76698 65.79775 69.58806 71.41346
> colSums(tmp5,na.rm=TRUE)
[1] 1020.0885 730.2526 676.1225 0.0000 620.4053 659.8564 644.8012
[8] 641.1556 641.2500 619.0953 672.4784 682.5248 655.1772 677.9941
[15] 647.3971 615.7229 591.9028 592.1798 626.2926 642.7211
> colVars(tmp5,na.rm=TRUE)
[1] 18137.86134 32.91205 101.35472 NA 130.98981 56.82282
[7] 26.71973 60.55890 78.20437 37.56782 160.94124 54.48188
[13] 134.02520 26.54527 97.19514 46.02348 16.08775 140.73203
[19] 60.48114 46.05279
> colSd(tmp5,na.rm=TRUE)
[1] 134.676878 5.736902 10.067508 NA 11.445078 7.538091
[7] 5.169113 7.781960 8.843324 6.129259 12.686262 7.381185
[13] 11.576925 5.152211 9.858759 6.784061 4.010954 11.863053
[19] 7.776962 6.786221
> colMax(tmp5,na.rm=TRUE)
[1] 472.04584 90.51591 89.12505 -Inf 89.45997 84.59577 80.95151
[8] 80.78677 84.17458 81.58963 90.14796 86.70422 87.86024 82.51301
[15] 90.89639 75.04715 71.61557 86.04481 77.03308 79.74335
> colMin(tmp5,na.rm=TRUE)
[1] 57.50800 72.08210 63.07802 Inf 55.09748 64.96003 62.57401 58.92131
[9] 58.23380 62.54678 53.33634 64.83818 56.71180 68.34511 61.55976 56.09870
[17] 59.39199 53.40112 55.55256 57.63615
>
>
>
>
> 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] 348.7376 264.9829 323.7880 249.1259 221.5876 186.2218 221.4015 257.0510
[9] 121.1466 167.7848
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 348.7376 264.9829 323.7880 249.1259 221.5876 186.2218 221.4015 257.0510
[9] 121.1466 167.7848
>
>
>
> 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 -5.684342e-14 5.684342e-14 4.263256e-14 -5.684342e-14
[6] 0.000000e+00 -2.842171e-14 1.136868e-13 2.842171e-14 0.000000e+00
[11] 1.136868e-13 5.684342e-14 1.705303e-13 5.684342e-14 8.526513e-14
[16] 5.684342e-14 -5.684342e-14 1.421085e-13 -2.842171e-13 5.684342e-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)
+ }
7 2
6 10
5 20
6 5
3 14
4 18
3 9
8 12
10 8
10 14
10 2
3 18
2 1
8 10
7 9
8 20
8 4
4 11
4 2
6 12
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] 1.978234
> Min(tmp)
[1] -2.350018
> mean(tmp)
[1] -0.03783472
> Sum(tmp)
[1] -3.783472
> Var(tmp)
[1] 0.7459877
>
> rowMeans(tmp)
[1] -0.03783472
> rowSums(tmp)
[1] -3.783472
> rowVars(tmp)
[1] 0.7459877
> rowSd(tmp)
[1] 0.8637058
> rowMax(tmp)
[1] 1.978234
> rowMin(tmp)
[1] -2.350018
>
> colMeans(tmp)
[1] -0.08424287 0.84160477 -1.56316144 0.33240647 -0.72945403 0.67680531
[7] 0.15191875 -0.12061342 -1.41036892 -0.29776146 0.37273868 -1.08470121
[13] -0.56741190 -1.58263224 1.17669463 0.40267433 1.37236821 0.15137559
[19] 0.02530509 1.97823370 0.09442808 0.22956833 -1.44103936 -0.37280848
[25] -0.12154609 -1.16790071 -0.64677880 0.68926841 -0.34459734 -0.44362528
[31] -0.55544236 -0.12334965 0.48879086 1.04981623 -0.09725874 -0.01378000
[37] 1.16894030 -0.84613057 -1.37733703 0.21636176 0.87028283 -1.46976951
[43] -0.65029025 -0.97429674 1.27287623 1.46194278 -2.35001753 -1.56819843
[49] 1.82879082 1.02724154 1.62373264 0.59767738 -0.06338200 0.30048672
[55] -0.36371804 0.13456519 -1.44479439 -0.17750265 0.05514862 0.16766669
[61] 0.22309260 -1.14968424 0.88871689 1.51327950 0.18161405 0.00512804
[67] -0.24951461 0.86530898 -0.56376342 -1.54994890 -0.20507940 1.26504105
[73] -1.25966831 0.03140949 -0.59201564 0.69881308 0.70618106 -1.09167672
[79] -0.50203943 0.09717908 -0.35690761 0.29331616 0.36674477 0.12020751
[85] -1.12406709 1.14073383 -0.32535820 0.81868415 -0.78078988 -0.01149768
[91] -0.10466435 -0.24946161 0.64705223 -0.04495522 0.48806260 -0.38796059
[97] 0.16569958 -0.66450452 0.15892170 0.04909972
> colSums(tmp)
[1] -0.08424287 0.84160477 -1.56316144 0.33240647 -0.72945403 0.67680531
[7] 0.15191875 -0.12061342 -1.41036892 -0.29776146 0.37273868 -1.08470121
[13] -0.56741190 -1.58263224 1.17669463 0.40267433 1.37236821 0.15137559
[19] 0.02530509 1.97823370 0.09442808 0.22956833 -1.44103936 -0.37280848
[25] -0.12154609 -1.16790071 -0.64677880 0.68926841 -0.34459734 -0.44362528
[31] -0.55544236 -0.12334965 0.48879086 1.04981623 -0.09725874 -0.01378000
[37] 1.16894030 -0.84613057 -1.37733703 0.21636176 0.87028283 -1.46976951
[43] -0.65029025 -0.97429674 1.27287623 1.46194278 -2.35001753 -1.56819843
[49] 1.82879082 1.02724154 1.62373264 0.59767738 -0.06338200 0.30048672
[55] -0.36371804 0.13456519 -1.44479439 -0.17750265 0.05514862 0.16766669
[61] 0.22309260 -1.14968424 0.88871689 1.51327950 0.18161405 0.00512804
[67] -0.24951461 0.86530898 -0.56376342 -1.54994890 -0.20507940 1.26504105
[73] -1.25966831 0.03140949 -0.59201564 0.69881308 0.70618106 -1.09167672
[79] -0.50203943 0.09717908 -0.35690761 0.29331616 0.36674477 0.12020751
[85] -1.12406709 1.14073383 -0.32535820 0.81868415 -0.78078988 -0.01149768
[91] -0.10466435 -0.24946161 0.64705223 -0.04495522 0.48806260 -0.38796059
[97] 0.16569958 -0.66450452 0.15892170 0.04909972
> 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] -0.08424287 0.84160477 -1.56316144 0.33240647 -0.72945403 0.67680531
[7] 0.15191875 -0.12061342 -1.41036892 -0.29776146 0.37273868 -1.08470121
[13] -0.56741190 -1.58263224 1.17669463 0.40267433 1.37236821 0.15137559
[19] 0.02530509 1.97823370 0.09442808 0.22956833 -1.44103936 -0.37280848
[25] -0.12154609 -1.16790071 -0.64677880 0.68926841 -0.34459734 -0.44362528
[31] -0.55544236 -0.12334965 0.48879086 1.04981623 -0.09725874 -0.01378000
[37] 1.16894030 -0.84613057 -1.37733703 0.21636176 0.87028283 -1.46976951
[43] -0.65029025 -0.97429674 1.27287623 1.46194278 -2.35001753 -1.56819843
[49] 1.82879082 1.02724154 1.62373264 0.59767738 -0.06338200 0.30048672
[55] -0.36371804 0.13456519 -1.44479439 -0.17750265 0.05514862 0.16766669
[61] 0.22309260 -1.14968424 0.88871689 1.51327950 0.18161405 0.00512804
[67] -0.24951461 0.86530898 -0.56376342 -1.54994890 -0.20507940 1.26504105
[73] -1.25966831 0.03140949 -0.59201564 0.69881308 0.70618106 -1.09167672
[79] -0.50203943 0.09717908 -0.35690761 0.29331616 0.36674477 0.12020751
[85] -1.12406709 1.14073383 -0.32535820 0.81868415 -0.78078988 -0.01149768
[91] -0.10466435 -0.24946161 0.64705223 -0.04495522 0.48806260 -0.38796059
[97] 0.16569958 -0.66450452 0.15892170 0.04909972
> colMin(tmp)
[1] -0.08424287 0.84160477 -1.56316144 0.33240647 -0.72945403 0.67680531
[7] 0.15191875 -0.12061342 -1.41036892 -0.29776146 0.37273868 -1.08470121
[13] -0.56741190 -1.58263224 1.17669463 0.40267433 1.37236821 0.15137559
[19] 0.02530509 1.97823370 0.09442808 0.22956833 -1.44103936 -0.37280848
[25] -0.12154609 -1.16790071 -0.64677880 0.68926841 -0.34459734 -0.44362528
[31] -0.55544236 -0.12334965 0.48879086 1.04981623 -0.09725874 -0.01378000
[37] 1.16894030 -0.84613057 -1.37733703 0.21636176 0.87028283 -1.46976951
[43] -0.65029025 -0.97429674 1.27287623 1.46194278 -2.35001753 -1.56819843
[49] 1.82879082 1.02724154 1.62373264 0.59767738 -0.06338200 0.30048672
[55] -0.36371804 0.13456519 -1.44479439 -0.17750265 0.05514862 0.16766669
[61] 0.22309260 -1.14968424 0.88871689 1.51327950 0.18161405 0.00512804
[67] -0.24951461 0.86530898 -0.56376342 -1.54994890 -0.20507940 1.26504105
[73] -1.25966831 0.03140949 -0.59201564 0.69881308 0.70618106 -1.09167672
[79] -0.50203943 0.09717908 -0.35690761 0.29331616 0.36674477 0.12020751
[85] -1.12406709 1.14073383 -0.32535820 0.81868415 -0.78078988 -0.01149768
[91] -0.10466435 -0.24946161 0.64705223 -0.04495522 0.48806260 -0.38796059
[97] 0.16569958 -0.66450452 0.15892170 0.04909972
> colMedians(tmp)
[1] -0.08424287 0.84160477 -1.56316144 0.33240647 -0.72945403 0.67680531
[7] 0.15191875 -0.12061342 -1.41036892 -0.29776146 0.37273868 -1.08470121
[13] -0.56741190 -1.58263224 1.17669463 0.40267433 1.37236821 0.15137559
[19] 0.02530509 1.97823370 0.09442808 0.22956833 -1.44103936 -0.37280848
[25] -0.12154609 -1.16790071 -0.64677880 0.68926841 -0.34459734 -0.44362528
[31] -0.55544236 -0.12334965 0.48879086 1.04981623 -0.09725874 -0.01378000
[37] 1.16894030 -0.84613057 -1.37733703 0.21636176 0.87028283 -1.46976951
[43] -0.65029025 -0.97429674 1.27287623 1.46194278 -2.35001753 -1.56819843
[49] 1.82879082 1.02724154 1.62373264 0.59767738 -0.06338200 0.30048672
[55] -0.36371804 0.13456519 -1.44479439 -0.17750265 0.05514862 0.16766669
[61] 0.22309260 -1.14968424 0.88871689 1.51327950 0.18161405 0.00512804
[67] -0.24951461 0.86530898 -0.56376342 -1.54994890 -0.20507940 1.26504105
[73] -1.25966831 0.03140949 -0.59201564 0.69881308 0.70618106 -1.09167672
[79] -0.50203943 0.09717908 -0.35690761 0.29331616 0.36674477 0.12020751
[85] -1.12406709 1.14073383 -0.32535820 0.81868415 -0.78078988 -0.01149768
[91] -0.10466435 -0.24946161 0.64705223 -0.04495522 0.48806260 -0.38796059
[97] 0.16569958 -0.66450452 0.15892170 0.04909972
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.08424287 0.8416048 -1.563161 0.3324065 -0.729454 0.6768053 0.1519187
[2,] -0.08424287 0.8416048 -1.563161 0.3324065 -0.729454 0.6768053 0.1519187
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.1206134 -1.410369 -0.2977615 0.3727387 -1.084701 -0.5674119 -1.582632
[2,] -0.1206134 -1.410369 -0.2977615 0.3727387 -1.084701 -0.5674119 -1.582632
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 1.176695 0.4026743 1.372368 0.1513756 0.02530509 1.978234 0.09442808
[2,] 1.176695 0.4026743 1.372368 0.1513756 0.02530509 1.978234 0.09442808
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.2295683 -1.441039 -0.3728085 -0.1215461 -1.167901 -0.6467788 0.6892684
[2,] 0.2295683 -1.441039 -0.3728085 -0.1215461 -1.167901 -0.6467788 0.6892684
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -0.3445973 -0.4436253 -0.5554424 -0.1233496 0.4887909 1.049816 -0.09725874
[2,] -0.3445973 -0.4436253 -0.5554424 -0.1233496 0.4887909 1.049816 -0.09725874
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -0.01378 1.16894 -0.8461306 -1.377337 0.2163618 0.8702828 -1.46977
[2,] -0.01378 1.16894 -0.8461306 -1.377337 0.2163618 0.8702828 -1.46977
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.6502903 -0.9742967 1.272876 1.461943 -2.350018 -1.568198 1.828791
[2,] -0.6502903 -0.9742967 1.272876 1.461943 -2.350018 -1.568198 1.828791
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 1.027242 1.623733 0.5976774 -0.063382 0.3004867 -0.363718 0.1345652
[2,] 1.027242 1.623733 0.5976774 -0.063382 0.3004867 -0.363718 0.1345652
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -1.444794 -0.1775026 0.05514862 0.1676667 0.2230926 -1.149684 0.8887169
[2,] -1.444794 -0.1775026 0.05514862 0.1676667 0.2230926 -1.149684 0.8887169
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 1.51328 0.1816141 0.00512804 -0.2495146 0.865309 -0.5637634 -1.549949
[2,] 1.51328 0.1816141 0.00512804 -0.2495146 0.865309 -0.5637634 -1.549949
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -0.2050794 1.265041 -1.259668 0.03140949 -0.5920156 0.6988131 0.7061811
[2,] -0.2050794 1.265041 -1.259668 0.03140949 -0.5920156 0.6988131 0.7061811
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -1.091677 -0.5020394 0.09717908 -0.3569076 0.2933162 0.3667448 0.1202075
[2,] -1.091677 -0.5020394 0.09717908 -0.3569076 0.2933162 0.3667448 0.1202075
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -1.124067 1.140734 -0.3253582 0.8186841 -0.7807899 -0.01149768 -0.1046644
[2,] -1.124067 1.140734 -0.3253582 0.8186841 -0.7807899 -0.01149768 -0.1046644
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -0.2494616 0.6470522 -0.04495522 0.4880626 -0.3879606 0.1656996 -0.6645045
[2,] -0.2494616 0.6470522 -0.04495522 0.4880626 -0.3879606 0.1656996 -0.6645045
[,99] [,100]
[1,] 0.1589217 0.04909972
[2,] 0.1589217 0.04909972
>
>
> Max(tmp2)
[1] 2.188123
> Min(tmp2)
[1] -3.080147
> mean(tmp2)
[1] 0.07584633
> Sum(tmp2)
[1] 7.584633
> Var(tmp2)
[1] 0.9982991
>
> rowMeans(tmp2)
[1] 0.271233173 0.017490987 0.111630763 0.001964354 0.953271388
[6] 1.810909535 -1.093339062 1.780546535 0.300259316 1.161847680
[11] -0.136334443 0.338755753 0.988845768 1.792033842 1.277173651
[16] 0.638919798 -1.574923421 -0.531371114 1.464217434 -0.559043813
[21] -0.987086426 0.177993859 -0.777376135 -1.548371544 0.691676569
[26] -0.613191964 0.066342626 -0.577929825 0.625927107 -0.992873685
[31] -0.104316221 -0.239033670 -0.191107286 0.703827293 -0.398755843
[36] -1.185129775 -0.741604951 0.827152495 -0.289395541 0.286126950
[41] -0.343213574 -0.570132307 0.927050355 -0.268958658 1.483553131
[46] 1.064274987 0.051889210 0.635475872 -0.962864571 -0.060475149
[51] 0.006839487 -0.536959392 -3.080147232 -0.834050747 -0.395130464
[56] 2.188122972 -0.056085938 -1.427207644 1.476218280 1.141043740
[61] 0.399145943 -0.430000690 1.152955493 0.693681556 -0.628247515
[66] -0.264285750 0.723460119 1.315817592 0.705411966 1.057335930
[71] -0.768537834 0.212233183 -1.909748885 0.581770062 -1.014024416
[76] -0.169601278 -0.505553926 0.692022747 1.719778312 -1.219703275
[81] 1.243545425 -0.231891926 2.044436325 -1.923450021 -0.142225652
[86] 0.165725763 -1.502472735 1.384257630 -0.530324486 -0.009717245
[91] 1.069045877 0.449118813 -0.720327708 -0.651473581 -1.708838740
[96] 1.660278273 -0.276317469 0.423800363 0.870922775 -0.559572915
> rowSums(tmp2)
[1] 0.271233173 0.017490987 0.111630763 0.001964354 0.953271388
[6] 1.810909535 -1.093339062 1.780546535 0.300259316 1.161847680
[11] -0.136334443 0.338755753 0.988845768 1.792033842 1.277173651
[16] 0.638919798 -1.574923421 -0.531371114 1.464217434 -0.559043813
[21] -0.987086426 0.177993859 -0.777376135 -1.548371544 0.691676569
[26] -0.613191964 0.066342626 -0.577929825 0.625927107 -0.992873685
[31] -0.104316221 -0.239033670 -0.191107286 0.703827293 -0.398755843
[36] -1.185129775 -0.741604951 0.827152495 -0.289395541 0.286126950
[41] -0.343213574 -0.570132307 0.927050355 -0.268958658 1.483553131
[46] 1.064274987 0.051889210 0.635475872 -0.962864571 -0.060475149
[51] 0.006839487 -0.536959392 -3.080147232 -0.834050747 -0.395130464
[56] 2.188122972 -0.056085938 -1.427207644 1.476218280 1.141043740
[61] 0.399145943 -0.430000690 1.152955493 0.693681556 -0.628247515
[66] -0.264285750 0.723460119 1.315817592 0.705411966 1.057335930
[71] -0.768537834 0.212233183 -1.909748885 0.581770062 -1.014024416
[76] -0.169601278 -0.505553926 0.692022747 1.719778312 -1.219703275
[81] 1.243545425 -0.231891926 2.044436325 -1.923450021 -0.142225652
[86] 0.165725763 -1.502472735 1.384257630 -0.530324486 -0.009717245
[91] 1.069045877 0.449118813 -0.720327708 -0.651473581 -1.708838740
[96] 1.660278273 -0.276317469 0.423800363 0.870922775 -0.559572915
> 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] 0.271233173 0.017490987 0.111630763 0.001964354 0.953271388
[6] 1.810909535 -1.093339062 1.780546535 0.300259316 1.161847680
[11] -0.136334443 0.338755753 0.988845768 1.792033842 1.277173651
[16] 0.638919798 -1.574923421 -0.531371114 1.464217434 -0.559043813
[21] -0.987086426 0.177993859 -0.777376135 -1.548371544 0.691676569
[26] -0.613191964 0.066342626 -0.577929825 0.625927107 -0.992873685
[31] -0.104316221 -0.239033670 -0.191107286 0.703827293 -0.398755843
[36] -1.185129775 -0.741604951 0.827152495 -0.289395541 0.286126950
[41] -0.343213574 -0.570132307 0.927050355 -0.268958658 1.483553131
[46] 1.064274987 0.051889210 0.635475872 -0.962864571 -0.060475149
[51] 0.006839487 -0.536959392 -3.080147232 -0.834050747 -0.395130464
[56] 2.188122972 -0.056085938 -1.427207644 1.476218280 1.141043740
[61] 0.399145943 -0.430000690 1.152955493 0.693681556 -0.628247515
[66] -0.264285750 0.723460119 1.315817592 0.705411966 1.057335930
[71] -0.768537834 0.212233183 -1.909748885 0.581770062 -1.014024416
[76] -0.169601278 -0.505553926 0.692022747 1.719778312 -1.219703275
[81] 1.243545425 -0.231891926 2.044436325 -1.923450021 -0.142225652
[86] 0.165725763 -1.502472735 1.384257630 -0.530324486 -0.009717245
[91] 1.069045877 0.449118813 -0.720327708 -0.651473581 -1.708838740
[96] 1.660278273 -0.276317469 0.423800363 0.870922775 -0.559572915
> rowMin(tmp2)
[1] 0.271233173 0.017490987 0.111630763 0.001964354 0.953271388
[6] 1.810909535 -1.093339062 1.780546535 0.300259316 1.161847680
[11] -0.136334443 0.338755753 0.988845768 1.792033842 1.277173651
[16] 0.638919798 -1.574923421 -0.531371114 1.464217434 -0.559043813
[21] -0.987086426 0.177993859 -0.777376135 -1.548371544 0.691676569
[26] -0.613191964 0.066342626 -0.577929825 0.625927107 -0.992873685
[31] -0.104316221 -0.239033670 -0.191107286 0.703827293 -0.398755843
[36] -1.185129775 -0.741604951 0.827152495 -0.289395541 0.286126950
[41] -0.343213574 -0.570132307 0.927050355 -0.268958658 1.483553131
[46] 1.064274987 0.051889210 0.635475872 -0.962864571 -0.060475149
[51] 0.006839487 -0.536959392 -3.080147232 -0.834050747 -0.395130464
[56] 2.188122972 -0.056085938 -1.427207644 1.476218280 1.141043740
[61] 0.399145943 -0.430000690 1.152955493 0.693681556 -0.628247515
[66] -0.264285750 0.723460119 1.315817592 0.705411966 1.057335930
[71] -0.768537834 0.212233183 -1.909748885 0.581770062 -1.014024416
[76] -0.169601278 -0.505553926 0.692022747 1.719778312 -1.219703275
[81] 1.243545425 -0.231891926 2.044436325 -1.923450021 -0.142225652
[86] 0.165725763 -1.502472735 1.384257630 -0.530324486 -0.009717245
[91] 1.069045877 0.449118813 -0.720327708 -0.651473581 -1.708838740
[96] 1.660278273 -0.276317469 0.423800363 0.870922775 -0.559572915
>
> colMeans(tmp2)
[1] 0.07584633
> colSums(tmp2)
[1] 7.584633
> colVars(tmp2)
[1] 0.9982991
> colSd(tmp2)
[1] 0.9991492
> colMax(tmp2)
[1] 2.188123
> colMin(tmp2)
[1] -3.080147
> colMedians(tmp2)
[1] 0.004401921
> colRanges(tmp2)
[,1]
[1,] -3.080147
[2,] 2.188123
>
> 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] 3.5716550 -2.1771377 9.8998155 -0.6836088 -1.4365532 1.8072373
[7] 1.7523073 -1.3304700 -4.3096590 3.4867345
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.4406123
[2,] -0.7237361
[3,] 0.5864901
[4,] 1.2900455
[5,] 2.1677524
>
> rowApply(tmp,sum)
[1] 2.1987312 -0.5147502 -2.5763146 -6.3137607 3.1675365 2.5502205
[7] 4.6350648 2.8766819 -0.4817118 5.0386234
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 7 9 6 4 1 10 1 8 8 10
[2,] 2 2 4 2 10 1 4 1 9 6
[3,] 10 10 10 10 7 3 9 6 3 8
[4,] 8 5 9 3 6 2 6 3 7 3
[5,] 1 7 2 6 4 8 7 4 5 4
[6,] 4 8 3 1 8 9 8 5 6 7
[7,] 5 4 8 7 5 5 10 9 2 5
[8,] 6 3 7 5 9 7 3 2 4 1
[9,] 9 1 1 8 2 4 2 10 1 2
[10,] 3 6 5 9 3 6 5 7 10 9
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 1.7338068 0.8901322 2.1867080 2.0836883 1.0479048 -1.2579101
[7] -0.3217398 3.1602671 -1.1168612 3.5872161 0.5166689 -0.8745405
[13] -2.4315242 0.8989620 -1.4202938 -0.5769417 1.4516586 -3.6636224
[19] -1.3642799 1.9858604
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.5257181
[2,] 0.2432566
[3,] 0.6105547
[4,] 1.0313013
[5,] 1.3744123
>
> rowApply(tmp,sum)
[1] 0.6597792 -5.7315156 3.4025833 -0.9752852 9.1595979
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 2 19 11 18 13
[2,] 8 6 15 19 11
[3,] 11 16 3 3 20
[4,] 18 17 5 11 7
[5,] 19 9 18 13 4
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -1.5257181 -0.1272495 0.2778125 1.1990127 1.3879443 -0.9396127
[2,] 1.3744123 -1.3343728 1.0605562 1.2725323 -0.9400505 -1.0770977
[3,] 0.2432566 0.5809022 -1.0020390 -0.4719278 1.2319931 -0.1566925
[4,] 1.0313013 1.2260988 -0.6867979 -0.1203315 0.1168676 -0.4089710
[5,] 0.6105547 0.5447536 2.5371762 0.2044025 -0.7488497 1.3244638
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.25145763 -0.9204645 0.89830696 0.6484486 0.2941182 0.8968226
[2,] -0.20469199 1.4671508 -0.63514153 0.8966079 0.7887847 -1.3848780
[3,] 0.69077015 1.9938839 -0.03512978 0.0269258 -0.4506027 -1.0546801
[4,] -0.04513819 -0.3068794 -0.58786519 0.1839352 -0.6257379 -0.5204727
[5,] -1.01413738 0.9265762 -0.75703166 1.8312986 0.5101065 1.1886676
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 1.9609202 -0.120671 -0.9099496 -1.1476706 0.71430216 -1.8130019
[2,] -1.6979981 -1.242439 -2.0805300 1.3007739 -0.03591959 -2.0609253
[3,] -1.3392477 1.799531 1.0630112 -0.6767811 -0.17030680 0.3659716
[4,] -1.2721468 -0.640982 0.8333625 -0.5034202 0.68651684 -1.0160718
[5,] -0.0830517 1.103523 -0.3261879 0.4501563 0.25706600 0.8604050
[,19] [,20]
[1,] 0.3721578 -0.7371865
[2,] -1.7076262 0.5093372
[3,] 0.5015304 0.2622149
[4,] 0.2835194 1.3979275
[5,] -0.8138612 0.5535673
>
>
> 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 : 653 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 : 565 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-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 -0.1121204 0.4149579 -3.236743 -0.9508915 -2.575234 -1.04047 0.8865631
col8 col9 col10 col11 col12 col13 col14
row1 -1.156788 -0.2547916 -0.8065363 -0.1595271 0.4207046 0.7179056 0.9220879
col15 col16 col17 col18 col19 col20
row1 -0.03017584 0.5288405 0.1600653 1.302712 -1.189959 0.1474994
> tmp[,"col10"]
col10
row1 -0.8065363
row2 -0.8079752
row3 -1.4223443
row4 -0.7277796
row5 -1.3441575
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 -0.1121204 0.4149579 -3.236743 -0.9508915 -2.575234 -1.0404700 0.8865631
row5 1.3323130 1.1061730 2.016295 -0.1734876 -2.288891 -0.8376238 -0.0743449
col8 col9 col10 col11 col12 col13 col14
row1 -1.1567881 -0.2547916 -0.8065363 -0.1595271 0.4207046 0.7179056 0.9220879
row5 0.3119084 -0.8918311 -1.3441575 -0.8588814 2.1465069 -0.7152991 0.7555505
col15 col16 col17 col18 col19 col20
row1 -0.03017584 0.5288405 0.1600653 1.3027125 -1.189959 0.1474994
row5 -1.04873819 0.6142597 0.3603614 -0.2008191 -1.020200 1.2366949
> tmp[,c("col6","col20")]
col6 col20
row1 -1.0404700 0.1474994
row2 0.8578379 1.5569032
row3 -1.2459250 -1.2283651
row4 -0.1467159 0.4237118
row5 -0.8376238 1.2366949
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -1.0404700 0.1474994
row5 -0.8376238 1.2366949
>
>
>
>
> 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 48.85659 48.81722 49.15955 50.83678 49.42829 103.7944 50.29978 50.14495
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.28455 48.38757 50.01832 49.22586 48.92632 49.661 50.01722 50.46668
col17 col18 col19 col20
row1 50.45372 50.22304 51.29885 103.924
> tmp[,"col10"]
col10
row1 48.38757
row2 30.33696
row3 29.11162
row4 29.14390
row5 48.82802
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 48.85659 48.81722 49.15955 50.83678 49.42829 103.7944 50.29978 50.14495
row5 49.19625 52.60551 48.45066 50.52032 48.48213 105.7508 49.93021 48.04557
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.28455 48.38757 50.01832 49.22586 48.92632 49.66100 50.01722 50.46668
row5 50.45410 48.82802 50.57911 50.53515 50.12908 49.75679 51.15330 49.50194
col17 col18 col19 col20
row1 50.45372 50.22304 51.29885 103.9240
row5 49.30601 50.56684 48.96862 105.3332
> tmp[,c("col6","col20")]
col6 col20
row1 103.79438 103.92401
row2 76.51253 73.81373
row3 74.50265 74.35771
row4 73.04445 74.72970
row5 105.75081 105.33315
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 103.7944 103.9240
row5 105.7508 105.3332
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 103.7944 103.9240
row5 105.7508 105.3332
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.4364864
[2,] -0.2551980
[3,] -0.5486590
[4,] -0.4588333
[5,] -0.2320870
> tmp[,c("col17","col7")]
col17 col7
[1,] 0.4346944 -0.7527071
[2,] 0.7363747 1.4006310
[3,] -1.8461743 -0.4746651
[4,] 1.2007153 -0.5677732
[5,] -0.5011905 -0.5578709
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 0.6901961 -0.7412357
[2,] -1.2317594 -0.4402000
[3,] 0.4598439 -0.2405585
[4,] -0.7665351 -0.2195621
[5,] 0.6302586 -0.3323281
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 0.6901961
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 0.6901961
[2,] -1.2317594
>
>
>
> 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 -0.5106566 -0.5197769 -0.5152784 0.1759479 -0.6900887 1.404732 -0.5106633
row1 0.2718119 1.1019742 -0.2839383 0.5399517 -1.3040400 0.515172 -1.3910422
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row3 -0.9947125 0.7456911 -1.0603541 0.9910694 0.8553962 -0.2374365 -0.9326369
row1 -0.1335936 0.7003187 0.7684134 2.4646117 1.3702687 -1.0598351 1.8029710
[,15] [,16] [,17] [,18] [,19] [,20]
row3 1.0495078 1.085252 -0.1487723 0.1850532 1.5162395 -0.9151125
row1 -0.6554031 -1.306111 0.1972403 -0.9202650 -0.2072972 -0.6220577
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -1.092537 -0.895083 0.2461237 1.061514 -0.866508 0.2941279 2.384877
[,8] [,9] [,10]
row2 0.8326437 0.6667588 0.608899
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -1.147645 -1.03425 -0.3190587 -0.8515079 -0.2992093 0.7000377 -1.198165
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.6748823 0.551486 -0.9927433 0.6771283 -0.3441139 -0.1920531 -0.1300078
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -1.469607 0.7412205 1.096027 -0.3736816 -1.263289 0.2634678
>
>
> 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: 0x5a6b8f8ccfa0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM26fdd47c6ef8e0"
[2] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM26fdd440566f80"
[3] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM26fdd4737aa6b0"
[4] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM26fdd4357f3843"
[5] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM26fdd4474d8dbb"
[6] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM26fdd46216a898"
[7] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM26fdd4770064a2"
[8] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM26fdd472a78fde"
[9] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM26fdd433dcba62"
[10] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM26fdd4786b432"
[11] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM26fdd42e9457f8"
[12] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM26fdd4175bdad4"
[13] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM26fdd45b45cf44"
[14] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM26fdd46e7ab06a"
[15] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM26fdd44415f719"
>
>
> ### 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: 0x5a6b8f72c3a0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x5a6b8f72c3a0>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x5a6b8f72c3a0>
> rowMedians(tmp)
[1] -0.445578602 0.229684677 -0.158393388 -0.478813237 -0.010708920
[6] -0.063941341 0.339475126 0.026235915 -0.049288218 -0.404948448
[11] -0.578025987 0.159402150 0.013199292 0.140753420 0.250771260
[16] -0.311315353 0.030059230 0.260909083 -0.155843925 -0.360252086
[21] 0.451351153 0.484912890 0.007205843 0.393485748 0.367125580
[26] -0.149953284 0.308586601 -0.222213520 0.086724944 -0.356236280
[31] 0.224740404 -0.152206013 0.150199327 0.059377604 0.236385462
[36] -0.029259446 -0.118368435 0.464915532 0.250635016 0.181125790
[41] 0.171618054 -0.044258272 -0.223995570 0.424022864 -0.104530723
[46] -0.439077800 0.337901750 -0.039032215 0.189301286 0.138596956
[51] 0.334818517 0.259009064 -0.172246486 0.105977720 -0.170412251
[56] 0.181248837 0.401052971 -0.159264037 0.138343060 0.421613402
[61] 0.034220200 -0.374218948 -0.187271992 0.055856889 0.358994835
[66] -0.447202551 0.011225283 0.715225562 -0.419338288 -0.334832424
[71] 0.283397122 -0.417985966 0.201013813 -0.516748739 0.366064188
[76] 0.207812368 0.023139673 0.311249712 0.177733827 -0.147523343
[81] 0.170475841 -0.092913938 -0.516839438 -0.067014135 0.492228111
[86] 0.614978141 0.488376974 0.174369326 0.341346784 0.220818304
[91] -0.297071244 -0.171226471 0.270326445 -0.306478799 -0.015740672
[96] -0.238589115 0.594929089 0.345078866 0.167831803 -0.208887063
[101] 0.385670109 0.737271193 -0.531418607 -0.348702841 0.672198533
[106] 0.283621325 0.206940388 -0.353842711 0.244635245 -0.483312411
[111] -0.338894177 -0.618593778 -0.234088148 0.168509003 0.027521214
[116] 0.022101975 0.179672821 0.116062671 0.026276349 0.379654261
[121] 0.159361398 -0.072172962 0.055421510 -0.558677577 -0.448682395
[126] 0.136834302 -0.080886438 -0.480797534 0.383397003 -0.008989179
[131] -0.013366275 -0.318257705 0.340691014 0.638286523 -0.201588074
[136] -0.623896465 -0.299271300 -0.182351904 0.077034569 0.225237134
[141] 0.154815797 -0.253471095 0.785448020 -0.041095106 -0.418503318
[146] 0.239804686 -0.412560649 -0.285242990 0.292304326 0.011034134
[151] 0.040137395 -0.108984249 0.393787075 -0.176065915 0.462125554
[156] -0.028183694 0.014123644 -0.035067133 0.404656322 0.047505541
[161] -0.223879084 0.383627861 0.203997791 -0.065003694 -0.147340493
[166] 0.101973571 0.253209378 -0.231426661 0.356906722 -0.150327027
[171] -0.182980475 0.484437398 -0.162574978 0.027969964 -0.925151719
[176] 0.022346794 -0.504547165 0.120810257 0.286932108 -0.219683561
[181] -0.217908382 0.034763816 0.591513585 -0.102152394 0.128570994
[186] 0.005452790 -0.227154996 -0.204954081 -0.207714689 0.299953655
[191] 0.322716993 -0.128098400 0.173073272 -0.438681739 -0.516452687
[196] 0.267593155 -0.075913229 -0.024258196 -0.381186937 -0.052649534
[201] -0.415349587 0.100987134 -0.500704872 -0.144624052 -0.227763443
[206] 0.259817467 0.267627981 -0.161739602 -0.096660656 -0.086242049
[211] -0.484629216 0.069444763 0.348796136 -0.346653896 -0.088436386
[216] 0.230543449 -0.338743812 0.608456026 -0.183041877 -0.284164980
[221] -0.333639350 0.100473831 -0.015085370 0.249115258 0.039934737
[226] -0.238364187 -0.407986707 0.127263936 -0.205676789 0.002920944
>
> proc.time()
user system elapsed
1.298 1.448 2.735
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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: 0x60b66d99fb20>
> .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: 0x60b66d99fb20>
> .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: 0x60b66d99fb20>
> .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: 0x60b66d99fb20>
> 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: 0x60b66d980410>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60b66d980410>
> .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: 0x60b66d980410>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60b66d980410>
> .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: 0x60b66d980410>
> 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: 0x60b66c22d7a0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60b66c22d7a0>
> .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: 0x60b66c22d7a0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x60b66c22d7a0>
> .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: 0x60b66c22d7a0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x60b66c22d7a0>
> .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: 0x60b66c22d7a0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x60b66c22d7a0>
> .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: 0x60b66c22d7a0>
> 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: 0x60b66d1ff680>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x60b66d1ff680>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60b66d1ff680>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60b66d1ff680>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile26fe64707a97a0" "BufferedMatrixFile26fe64ec3abd0"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile26fe64707a97a0" "BufferedMatrixFile26fe64ec3abd0"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x60b66cf93490>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60b66cf93490>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x60b66cf93490>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x60b66cf93490>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x60b66cf93490>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x60b66cf93490>
> .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: 0x60b66e5ef110>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60b66e5ef110>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x60b66e5ef110>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x60b66e5ef110>
> 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: 0x60b66e6925e0>
> .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: 0x60b66e6925e0>
> rm(P)
>
> proc.time()
user system elapsed
0.249 0.043 0.282
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu
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Type 'license()' or 'licence()' for distribution details.
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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
0.248 0.040 0.277