| Back to Build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-01 07:38:36 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| 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 | ||||
|
To the developers/maintainers of the BufferedMatrix package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 228/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.63.0 (landing page) Ben Bolstad
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: BufferedMatrix |
| Version: 1.63.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings BufferedMatrix_1.63.0.tar.gz |
| StartedAt: 2023-02-27 22:24:33 -0000 (Mon, 27 Feb 2023) |
| EndedAt: 2023-02-27 22:25:08 -0000 (Mon, 27 Feb 2023) |
| EllapsedTime: 35.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings BufferedMatrix_1.63.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.63.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BufferedMatrix’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 R 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 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
prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword
prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details
prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value
prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references
prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso
prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘Rcodetesting.R’
Running ‘c_code_level_tests.R’
Running ‘objectTesting.R’
Running ‘rawCalltesting.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘BufferedMatrix.Rnw’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘BufferedMatrix’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function ‘dbm_ReadOnlyMode’:
doubleBufferedMatrix.c:1580:7: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
1580 | if (!(Matrix->readonly) & setting){
| ^~~~~~~~~~~~~~~~~~~
At top level:
doubleBufferedMatrix.c:3327:12: warning: ‘sort_double’ defined but not used [-Wunused-function]
3327 | static int sort_double(const double *a1,const double *a2){
| ^~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c init_package.c -o init_package.o
gcc -shared -L/home/biocbuild/bbs-3.17-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-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/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) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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
0.312 0.060 0.356
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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-3.17-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 456993 24.5 979984 52.4 651420 34.8
Vcells 842364 6.5 8388608 64.0 2047783 15.7
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Mon Feb 27 22:24:56 2023"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Mon Feb 27 22:24:56 2023"
>
>
> 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: 0xaaaadfcfe910>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Mon Feb 27 22:24:56 2023"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Mon Feb 27 22:24:57 2023"
>
> ColMode(tmp2)
<pointer: 0xaaaadfcfe910>
>
>
>
> ### 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,] 101.0058540 0.3425169 -0.7071951 -0.2439449
[2,] 0.6481443 0.4679637 0.2525855 -0.7956034
[3,] -0.1036408 1.0612600 0.3865258 0.8723081
[4,] 1.5160232 -0.1815400 2.4171743 0.5772204
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.17-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,] 101.0058540 0.3425169 0.7071951 0.2439449
[2,] 0.6481443 0.4679637 0.2525855 0.7956034
[3,] 0.1036408 1.0612600 0.3865258 0.8723081
[4,] 1.5160232 0.1815400 2.4171743 0.5772204
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.17-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,] 10.0501669 0.5852494 0.8409489 0.4939078
[2,] 0.8050741 0.6840787 0.5025789 0.8919660
[3,] 0.3219330 1.0301748 0.6217120 0.9339744
[4,] 1.2312689 0.4260751 1.5547265 0.7597502
>
> 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-3.17-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,] 226.50752 31.19501 34.11668 30.18302
[2,] 33.69889 32.30875 30.27837 34.71526
[3,] 28.32297 36.36301 31.60365 35.21205
[4,] 38.82871 29.44229 42.96444 33.17472
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0xaaaadf47d470>
> exp(tmp5)
<pointer: 0xaaaadf47d470>
> log(tmp5,2)
<pointer: 0xaaaadf47d470>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 471.4457
> Min(tmp5)
[1] 52.32604
> mean(tmp5)
[1] 71.66483
> Sum(tmp5)
[1] 14332.97
> Var(tmp5)
[1] 873.9415
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 89.27519 67.93856 71.24112 69.18783 71.12019 68.48372 71.27509 70.45295
[9] 68.89948 68.77411
> rowSums(tmp5)
[1] 1785.504 1358.771 1424.822 1383.757 1422.404 1369.674 1425.502 1409.059
[9] 1377.990 1375.482
> rowVars(tmp5)
[1] 8135.42504 29.29291 87.24806 75.35462 73.62717 70.01289
[7] 75.30278 66.89166 95.68969 67.31568
> rowSd(tmp5)
[1] 90.196591 5.412293 9.340667 8.680704 8.580628 8.367371 8.677717
[8] 8.178732 9.782111 8.204614
> rowMax(tmp5)
[1] 471.44573 79.70666 89.15138 89.42485 86.23976 84.71521 84.85976
[8] 83.81819 87.25386 88.12162
> rowMin(tmp5)
[1] 60.24759 58.03189 57.38319 56.99107 55.97312 54.84357 55.89281 56.00538
[9] 52.32604 55.26769
>
> colMeans(tmp5)
[1] 109.18131 68.37462 69.60122 65.76353 71.69504 73.87278 71.35336
[8] 69.38622 68.89793 68.97179 67.24146 71.68069 74.66434 72.65759
[15] 69.83977 65.65036 68.24578 70.91509 70.46738 64.83624
> colSums(tmp5)
[1] 1091.8131 683.7462 696.0122 657.6353 716.9504 738.7278 713.5336
[8] 693.8622 688.9793 689.7179 672.4146 716.8069 746.6434 726.5759
[15] 698.3977 656.5036 682.4578 709.1509 704.6738 648.3624
> colVars(tmp5)
[1] 16267.09249 109.89915 94.25452 30.17062 85.25270 49.77112
[7] 63.11682 112.59284 65.17221 38.51946 48.69157 46.39289
[13] 36.46387 122.53776 79.49633 21.85959 68.44647 63.72149
[19] 33.63100 95.80283
> colSd(tmp5)
[1] 127.542512 10.483279 9.708477 5.492779 9.233239 7.054865
[7] 7.944609 10.610977 8.072931 6.206404 6.977934 6.811233
[13] 6.038532 11.069677 8.916071 4.675424 8.273238 7.982574
[19] 5.799224 9.787892
> colMax(tmp5)
[1] 471.44573 88.12162 89.42485 73.28927 83.81819 83.36582 84.85976
[8] 89.15138 81.00491 77.64760 80.67186 80.75170 84.56021 87.25386
[15] 84.65388 73.12618 81.61364 82.55299 81.57293 80.68423
> colMin(tmp5)
[1] 55.89281 52.32604 56.00232 55.97312 61.13262 61.91752 60.66811 56.76752
[9] 55.26769 60.24759 58.03593 60.90687 67.04953 57.71037 54.84357 57.76653
[17] 58.79411 56.99107 60.23055 54.32206
>
>
> ### 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] NA 67.93856 71.24112 69.18783 71.12019 68.48372 71.27509 70.45295
[9] 68.89948 68.77411
> rowSums(tmp5)
[1] NA 1358.771 1424.822 1383.757 1422.404 1369.674 1425.502 1409.059
[9] 1377.990 1375.482
> rowVars(tmp5)
[1] 8557.17005 29.29291 87.24806 75.35462 73.62717 70.01289
[7] 75.30278 66.89166 95.68969 67.31568
> rowSd(tmp5)
[1] 92.504973 5.412293 9.340667 8.680704 8.580628 8.367371 8.677717
[8] 8.178732 9.782111 8.204614
> rowMax(tmp5)
[1] NA 79.70666 89.15138 89.42485 86.23976 84.71521 84.85976 83.81819
[9] 87.25386 88.12162
> rowMin(tmp5)
[1] NA 58.03189 57.38319 56.99107 55.97312 54.84357 55.89281 56.00538
[9] 52.32604 55.26769
>
> colMeans(tmp5)
[1] 109.18131 68.37462 69.60122 65.76353 71.69504 73.87278 71.35336
[8] 69.38622 68.89793 68.97179 67.24146 71.68069 74.66434 NA
[15] 69.83977 65.65036 68.24578 70.91509 70.46738 64.83624
> colSums(tmp5)
[1] 1091.8131 683.7462 696.0122 657.6353 716.9504 738.7278 713.5336
[8] 693.8622 688.9793 689.7179 672.4146 716.8069 746.6434 NA
[15] 698.3977 656.5036 682.4578 709.1509 704.6738 648.3624
> colVars(tmp5)
[1] 16267.09249 109.89915 94.25452 30.17062 85.25270 49.77112
[7] 63.11682 112.59284 65.17221 38.51946 48.69157 46.39289
[13] 36.46387 NA 79.49633 21.85959 68.44647 63.72149
[19] 33.63100 95.80283
> colSd(tmp5)
[1] 127.542512 10.483279 9.708477 5.492779 9.233239 7.054865
[7] 7.944609 10.610977 8.072931 6.206404 6.977934 6.811233
[13] 6.038532 NA 8.916071 4.675424 8.273238 7.982574
[19] 5.799224 9.787892
> colMax(tmp5)
[1] 471.44573 88.12162 89.42485 73.28927 83.81819 83.36582 84.85976
[8] 89.15138 81.00491 77.64760 80.67186 80.75170 84.56021 NA
[15] 84.65388 73.12618 81.61364 82.55299 81.57293 80.68423
> colMin(tmp5)
[1] 55.89281 52.32604 56.00232 55.97312 61.13262 61.91752 60.66811 56.76752
[9] 55.26769 60.24759 58.03593 60.90687 67.04953 NA 54.84357 57.76653
[17] 58.79411 56.99107 60.23055 54.32206
>
> Max(tmp5,na.rm=TRUE)
[1] 471.4457
> Min(tmp5,na.rm=TRUE)
[1] 52.32604
> mean(tmp5,na.rm=TRUE)
[1] 71.69057
> Sum(tmp5,na.rm=TRUE)
[1] 14266.42
> Var(tmp5,na.rm=TRUE)
[1] 878.2221
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.47170 67.93856 71.24112 69.18783 71.12019 68.48372 71.27509 70.45295
[9] 68.89948 68.77411
> rowSums(tmp5,na.rm=TRUE)
[1] 1718.962 1358.771 1424.822 1383.757 1422.404 1369.674 1425.502 1409.059
[9] 1377.990 1375.482
> rowVars(tmp5,na.rm=TRUE)
[1] 8557.17005 29.29291 87.24806 75.35462 73.62717 70.01289
[7] 75.30278 66.89166 95.68969 67.31568
> rowSd(tmp5,na.rm=TRUE)
[1] 92.504973 5.412293 9.340667 8.680704 8.580628 8.367371 8.677717
[8] 8.178732 9.782111 8.204614
> rowMax(tmp5,na.rm=TRUE)
[1] 471.44573 79.70666 89.15138 89.42485 86.23976 84.71521 84.85976
[8] 83.81819 87.25386 88.12162
> rowMin(tmp5,na.rm=TRUE)
[1] 60.24759 58.03189 57.38319 56.99107 55.97312 54.84357 55.89281 56.00538
[9] 52.32604 55.26769
>
> colMeans(tmp5,na.rm=TRUE)
[1] 109.18131 68.37462 69.60122 65.76353 71.69504 73.87278 71.35336
[8] 69.38622 68.89793 68.97179 67.24146 71.68069 74.66434 73.33714
[15] 69.83977 65.65036 68.24578 70.91509 70.46738 64.83624
> colSums(tmp5,na.rm=TRUE)
[1] 1091.8131 683.7462 696.0122 657.6353 716.9504 738.7278 713.5336
[8] 693.8622 688.9793 689.7179 672.4146 716.8069 746.6434 660.0343
[15] 698.3977 656.5036 682.4578 709.1509 704.6738 648.3624
> colVars(tmp5,na.rm=TRUE)
[1] 16267.09249 109.89915 94.25452 30.17062 85.25270 49.77112
[7] 63.11682 112.59284 65.17221 38.51946 48.69157 46.39289
[13] 36.46387 132.65986 79.49633 21.85959 68.44647 63.72149
[19] 33.63100 95.80283
> colSd(tmp5,na.rm=TRUE)
[1] 127.542512 10.483279 9.708477 5.492779 9.233239 7.054865
[7] 7.944609 10.610977 8.072931 6.206404 6.977934 6.811233
[13] 6.038532 11.517806 8.916071 4.675424 8.273238 7.982574
[19] 5.799224 9.787892
> colMax(tmp5,na.rm=TRUE)
[1] 471.44573 88.12162 89.42485 73.28927 83.81819 83.36582 84.85976
[8] 89.15138 81.00491 77.64760 80.67186 80.75170 84.56021 87.25386
[15] 84.65388 73.12618 81.61364 82.55299 81.57293 80.68423
> colMin(tmp5,na.rm=TRUE)
[1] 55.89281 52.32604 56.00232 55.97312 61.13262 61.91752 60.66811 56.76752
[9] 55.26769 60.24759 58.03593 60.90687 67.04953 57.71037 54.84357 57.76653
[17] 58.79411 56.99107 60.23055 54.32206
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] NaN 67.93856 71.24112 69.18783 71.12019 68.48372 71.27509 70.45295
[9] 68.89948 68.77411
> rowSums(tmp5,na.rm=TRUE)
[1] 0.000 1358.771 1424.822 1383.757 1422.404 1369.674 1425.502 1409.059
[9] 1377.990 1375.482
> rowVars(tmp5,na.rm=TRUE)
[1] NA 29.29291 87.24806 75.35462 73.62717 70.01289 75.30278 66.89166
[9] 95.68969 67.31568
> rowSd(tmp5,na.rm=TRUE)
[1] NA 5.412293 9.340667 8.680704 8.580628 8.367371 8.677717 8.178732
[9] 9.782111 8.204614
> rowMax(tmp5,na.rm=TRUE)
[1] NA 79.70666 89.15138 89.42485 86.23976 84.71521 84.85976 83.81819
[9] 87.25386 88.12162
> rowMin(tmp5,na.rm=TRUE)
[1] NA 58.03189 57.38319 56.99107 55.97312 54.84357 55.89281 56.00538
[9] 52.32604 55.26769
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 68.92971 68.75754 69.44476 66.09037 71.66675 75.20114 72.41368 68.81042
[9] 68.30734 69.94115 67.74381 70.78117 73.74483 NaN 69.83033 65.58486
[17] 68.26078 71.93237 69.98107 63.40315
> colSums(tmp5,na.rm=TRUE)
[1] 620.3674 618.8179 625.0028 594.8133 645.0007 676.8103 651.7231 619.2937
[9] 614.7660 629.4703 609.6943 637.0305 663.7035 0.0000 628.4730 590.2637
[17] 614.3470 647.3913 629.8296 570.6284
> colVars(tmp5,na.rm=TRUE)
[1] 73.32470 121.98697 105.76092 32.74020 95.90028 36.14136 58.35827
[8] 122.93696 69.39478 32.76332 51.93900 43.08925 31.51006 NA
[15] 89.43236 24.54376 76.99975 60.04470 35.17431 84.67359
> colSd(tmp5,na.rm=TRUE)
[1] 8.562984 11.044771 10.284013 5.721905 9.792869 6.011768 7.639259
[8] 11.087694 8.330353 5.723925 7.206871 6.564241 5.613382 NA
[15] 9.456869 4.954166 8.774950 7.748851 5.930794 9.201825
> colMax(tmp5,na.rm=TRUE)
[1] 80.81688 88.12162 89.42485 73.28927 83.81819 83.36582 84.85976 89.15138
[9] 81.00491 77.64760 80.67186 80.75170 84.56021 -Inf 84.65388 73.12618
[17] 81.61364 82.55299 81.57293 80.68423
> colMin(tmp5,na.rm=TRUE)
[1] 55.89281 52.32604 56.00232 55.97312 61.13262 63.67544 60.66811 56.76752
[9] 55.26769 61.72965 58.03593 60.90687 67.04953 Inf 54.84357 57.76653
[17] 58.79411 56.99107 60.23055 54.32206
>
>
>
>
> 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] 189.1673 274.8387 155.0119 336.0750 148.2390 216.4087 219.4313 183.4329
[9] 199.7169 285.9391
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 189.1673 274.8387 155.0119 336.0750 148.2390 216.4087 219.4313 183.4329
[9] 199.7169 285.9391
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] 2.842171e-14 1.705303e-13 -1.136868e-13 -4.263256e-14 -1.421085e-13
[6] -2.842171e-14 -5.684342e-14 -5.684342e-14 1.989520e-13 2.273737e-13
[11] -2.273737e-13 5.684342e-14 1.136868e-13 2.842171e-14 -9.947598e-14
[16] 0.000000e+00 1.421085e-13 -1.136868e-13 -2.842171e-14 0.000000e+00
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
10 19
1 7
6 9
5 3
2 12
7 15
5 15
1 2
4 16
6 8
10 12
8 18
10 7
8 17
3 6
1 17
8 7
1 6
2 15
6 9
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] 2.448771
> Min(tmp)
[1] -3.006815
> mean(tmp)
[1] 0.005668239
> Sum(tmp)
[1] 0.5668239
> Var(tmp)
[1] 1.074549
>
> rowMeans(tmp)
[1] 0.005668239
> rowSums(tmp)
[1] 0.5668239
> rowVars(tmp)
[1] 1.074549
> rowSd(tmp)
[1] 1.036605
> rowMax(tmp)
[1] 2.448771
> rowMin(tmp)
[1] -3.006815
>
> colMeans(tmp)
[1] 0.78030718 1.33624082 -3.00681525 0.62505538 0.06432584 0.54150564
[7] 0.34756151 1.49732080 -0.82922830 2.34094691 -0.49578338 -0.79155558
[13] 0.44978819 -0.29468920 -2.31695888 0.55629279 -0.30958436 0.55690342
[19] 0.42100938 -1.21186156 0.15239859 1.16750357 -0.52649031 -0.97667345
[25] 0.16432259 0.10138056 0.62621134 -0.67810933 0.16528874 -0.28141101
[31] -1.04345528 1.45366604 0.16790660 -1.56045587 1.03932390 -1.50679066
[37] -0.41296078 1.36003509 1.41672904 -0.05158097 0.67791343 -0.53780649
[43] 0.13050935 2.36696333 0.48892716 -1.46734638 0.05025867 0.35704154
[49] 0.44279194 0.01151796 0.55500610 0.54503452 0.30158921 0.06571920
[55] 2.44877107 0.27106999 0.02225208 -2.07458958 1.32832828 -0.18596553
[61] 1.13463729 1.19835366 1.49413134 0.07208254 -0.30053620 -0.71928433
[67] -0.68802039 0.24161123 -0.59088197 -1.15356739 -1.71202889 0.29496952
[73] -0.81743895 -1.09390503 0.42303082 -1.57066977 0.82728984 -1.05504324
[79] 0.90455690 -0.48917707 0.43882943 -0.30931377 0.15401483 -0.26446092
[85] 0.24196197 -0.70758356 -0.04339213 -0.15096078 1.11870459 -1.41458625
[91] -0.13274409 0.67358116 0.36064705 -0.85748947 0.60473672 1.76115409
[97] -2.77454731 -0.01856559 0.42654423 -1.77542180
> colSums(tmp)
[1] 0.78030718 1.33624082 -3.00681525 0.62505538 0.06432584 0.54150564
[7] 0.34756151 1.49732080 -0.82922830 2.34094691 -0.49578338 -0.79155558
[13] 0.44978819 -0.29468920 -2.31695888 0.55629279 -0.30958436 0.55690342
[19] 0.42100938 -1.21186156 0.15239859 1.16750357 -0.52649031 -0.97667345
[25] 0.16432259 0.10138056 0.62621134 -0.67810933 0.16528874 -0.28141101
[31] -1.04345528 1.45366604 0.16790660 -1.56045587 1.03932390 -1.50679066
[37] -0.41296078 1.36003509 1.41672904 -0.05158097 0.67791343 -0.53780649
[43] 0.13050935 2.36696333 0.48892716 -1.46734638 0.05025867 0.35704154
[49] 0.44279194 0.01151796 0.55500610 0.54503452 0.30158921 0.06571920
[55] 2.44877107 0.27106999 0.02225208 -2.07458958 1.32832828 -0.18596553
[61] 1.13463729 1.19835366 1.49413134 0.07208254 -0.30053620 -0.71928433
[67] -0.68802039 0.24161123 -0.59088197 -1.15356739 -1.71202889 0.29496952
[73] -0.81743895 -1.09390503 0.42303082 -1.57066977 0.82728984 -1.05504324
[79] 0.90455690 -0.48917707 0.43882943 -0.30931377 0.15401483 -0.26446092
[85] 0.24196197 -0.70758356 -0.04339213 -0.15096078 1.11870459 -1.41458625
[91] -0.13274409 0.67358116 0.36064705 -0.85748947 0.60473672 1.76115409
[97] -2.77454731 -0.01856559 0.42654423 -1.77542180
> 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] 0.78030718 1.33624082 -3.00681525 0.62505538 0.06432584 0.54150564
[7] 0.34756151 1.49732080 -0.82922830 2.34094691 -0.49578338 -0.79155558
[13] 0.44978819 -0.29468920 -2.31695888 0.55629279 -0.30958436 0.55690342
[19] 0.42100938 -1.21186156 0.15239859 1.16750357 -0.52649031 -0.97667345
[25] 0.16432259 0.10138056 0.62621134 -0.67810933 0.16528874 -0.28141101
[31] -1.04345528 1.45366604 0.16790660 -1.56045587 1.03932390 -1.50679066
[37] -0.41296078 1.36003509 1.41672904 -0.05158097 0.67791343 -0.53780649
[43] 0.13050935 2.36696333 0.48892716 -1.46734638 0.05025867 0.35704154
[49] 0.44279194 0.01151796 0.55500610 0.54503452 0.30158921 0.06571920
[55] 2.44877107 0.27106999 0.02225208 -2.07458958 1.32832828 -0.18596553
[61] 1.13463729 1.19835366 1.49413134 0.07208254 -0.30053620 -0.71928433
[67] -0.68802039 0.24161123 -0.59088197 -1.15356739 -1.71202889 0.29496952
[73] -0.81743895 -1.09390503 0.42303082 -1.57066977 0.82728984 -1.05504324
[79] 0.90455690 -0.48917707 0.43882943 -0.30931377 0.15401483 -0.26446092
[85] 0.24196197 -0.70758356 -0.04339213 -0.15096078 1.11870459 -1.41458625
[91] -0.13274409 0.67358116 0.36064705 -0.85748947 0.60473672 1.76115409
[97] -2.77454731 -0.01856559 0.42654423 -1.77542180
> colMin(tmp)
[1] 0.78030718 1.33624082 -3.00681525 0.62505538 0.06432584 0.54150564
[7] 0.34756151 1.49732080 -0.82922830 2.34094691 -0.49578338 -0.79155558
[13] 0.44978819 -0.29468920 -2.31695888 0.55629279 -0.30958436 0.55690342
[19] 0.42100938 -1.21186156 0.15239859 1.16750357 -0.52649031 -0.97667345
[25] 0.16432259 0.10138056 0.62621134 -0.67810933 0.16528874 -0.28141101
[31] -1.04345528 1.45366604 0.16790660 -1.56045587 1.03932390 -1.50679066
[37] -0.41296078 1.36003509 1.41672904 -0.05158097 0.67791343 -0.53780649
[43] 0.13050935 2.36696333 0.48892716 -1.46734638 0.05025867 0.35704154
[49] 0.44279194 0.01151796 0.55500610 0.54503452 0.30158921 0.06571920
[55] 2.44877107 0.27106999 0.02225208 -2.07458958 1.32832828 -0.18596553
[61] 1.13463729 1.19835366 1.49413134 0.07208254 -0.30053620 -0.71928433
[67] -0.68802039 0.24161123 -0.59088197 -1.15356739 -1.71202889 0.29496952
[73] -0.81743895 -1.09390503 0.42303082 -1.57066977 0.82728984 -1.05504324
[79] 0.90455690 -0.48917707 0.43882943 -0.30931377 0.15401483 -0.26446092
[85] 0.24196197 -0.70758356 -0.04339213 -0.15096078 1.11870459 -1.41458625
[91] -0.13274409 0.67358116 0.36064705 -0.85748947 0.60473672 1.76115409
[97] -2.77454731 -0.01856559 0.42654423 -1.77542180
> colMedians(tmp)
[1] 0.78030718 1.33624082 -3.00681525 0.62505538 0.06432584 0.54150564
[7] 0.34756151 1.49732080 -0.82922830 2.34094691 -0.49578338 -0.79155558
[13] 0.44978819 -0.29468920 -2.31695888 0.55629279 -0.30958436 0.55690342
[19] 0.42100938 -1.21186156 0.15239859 1.16750357 -0.52649031 -0.97667345
[25] 0.16432259 0.10138056 0.62621134 -0.67810933 0.16528874 -0.28141101
[31] -1.04345528 1.45366604 0.16790660 -1.56045587 1.03932390 -1.50679066
[37] -0.41296078 1.36003509 1.41672904 -0.05158097 0.67791343 -0.53780649
[43] 0.13050935 2.36696333 0.48892716 -1.46734638 0.05025867 0.35704154
[49] 0.44279194 0.01151796 0.55500610 0.54503452 0.30158921 0.06571920
[55] 2.44877107 0.27106999 0.02225208 -2.07458958 1.32832828 -0.18596553
[61] 1.13463729 1.19835366 1.49413134 0.07208254 -0.30053620 -0.71928433
[67] -0.68802039 0.24161123 -0.59088197 -1.15356739 -1.71202889 0.29496952
[73] -0.81743895 -1.09390503 0.42303082 -1.57066977 0.82728984 -1.05504324
[79] 0.90455690 -0.48917707 0.43882943 -0.30931377 0.15401483 -0.26446092
[85] 0.24196197 -0.70758356 -0.04339213 -0.15096078 1.11870459 -1.41458625
[91] -0.13274409 0.67358116 0.36064705 -0.85748947 0.60473672 1.76115409
[97] -2.77454731 -0.01856559 0.42654423 -1.77542180
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.7803072 1.336241 -3.006815 0.6250554 0.06432584 0.5415056 0.3475615
[2,] 0.7803072 1.336241 -3.006815 0.6250554 0.06432584 0.5415056 0.3475615
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 1.497321 -0.8292283 2.340947 -0.4957834 -0.7915556 0.4497882 -0.2946892
[2,] 1.497321 -0.8292283 2.340947 -0.4957834 -0.7915556 0.4497882 -0.2946892
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -2.316959 0.5562928 -0.3095844 0.5569034 0.4210094 -1.211862 0.1523986
[2,] -2.316959 0.5562928 -0.3095844 0.5569034 0.4210094 -1.211862 0.1523986
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 1.167504 -0.5264903 -0.9766735 0.1643226 0.1013806 0.6262113 -0.6781093
[2,] 1.167504 -0.5264903 -0.9766735 0.1643226 0.1013806 0.6262113 -0.6781093
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.1652887 -0.281411 -1.043455 1.453666 0.1679066 -1.560456 1.039324
[2,] 0.1652887 -0.281411 -1.043455 1.453666 0.1679066 -1.560456 1.039324
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -1.506791 -0.4129608 1.360035 1.416729 -0.05158097 0.6779134 -0.5378065
[2,] -1.506791 -0.4129608 1.360035 1.416729 -0.05158097 0.6779134 -0.5378065
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.1305094 2.366963 0.4889272 -1.467346 0.05025867 0.3570415 0.4427919
[2,] 0.1305094 2.366963 0.4889272 -1.467346 0.05025867 0.3570415 0.4427919
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.01151796 0.5550061 0.5450345 0.3015892 0.0657192 2.448771 0.27107
[2,] 0.01151796 0.5550061 0.5450345 0.3015892 0.0657192 2.448771 0.27107
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.02225208 -2.07459 1.328328 -0.1859655 1.134637 1.198354 1.494131
[2,] 0.02225208 -2.07459 1.328328 -0.1859655 1.134637 1.198354 1.494131
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.07208254 -0.3005362 -0.7192843 -0.6880204 0.2416112 -0.590882 -1.153567
[2,] 0.07208254 -0.3005362 -0.7192843 -0.6880204 0.2416112 -0.590882 -1.153567
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -1.712029 0.2949695 -0.8174389 -1.093905 0.4230308 -1.57067 0.8272898
[2,] -1.712029 0.2949695 -0.8174389 -1.093905 0.4230308 -1.57067 0.8272898
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -1.055043 0.9045569 -0.4891771 0.4388294 -0.3093138 0.1540148 -0.2644609
[2,] -1.055043 0.9045569 -0.4891771 0.4388294 -0.3093138 0.1540148 -0.2644609
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 0.241962 -0.7075836 -0.04339213 -0.1509608 1.118705 -1.414586 -0.1327441
[2,] 0.241962 -0.7075836 -0.04339213 -0.1509608 1.118705 -1.414586 -0.1327441
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 0.6735812 0.3606471 -0.8574895 0.6047367 1.761154 -2.774547 -0.01856559
[2,] 0.6735812 0.3606471 -0.8574895 0.6047367 1.761154 -2.774547 -0.01856559
[,99] [,100]
[1,] 0.4265442 -1.775422
[2,] 0.4265442 -1.775422
>
>
> Max(tmp2)
[1] 2.120442
> Min(tmp2)
[1] -2.264134
> mean(tmp2)
[1] -0.07750044
> Sum(tmp2)
[1] -7.750044
> Var(tmp2)
[1] 0.8060876
>
> rowMeans(tmp2)
[1] 1.268656816 -1.390924920 -0.095787611 -0.299043983 0.029618136
[6] -0.127087322 -0.074288563 -1.612409717 -0.462238369 -0.712800230
[11] 0.626164353 2.120442285 0.585654750 0.827579860 -1.304491394
[16] 0.884779691 -0.761047932 -0.444865622 0.227676281 0.007179428
[21] -0.509941644 -0.263039050 1.862931760 0.008842624 0.321902244
[26] 0.008534058 0.587884538 1.121518054 -1.809589241 0.351236167
[31] 1.246945355 0.946463709 0.205562918 -1.004508958 0.300687120
[36] 0.217996390 0.349889166 0.035803698 1.142626755 -0.658011835
[41] -0.241704010 -0.770561660 -0.852601828 0.469394916 0.834106828
[46] 0.342531117 0.874527093 -0.315187279 0.359189619 -0.145479408
[51] 1.434143401 1.021796070 -0.183935589 0.666162656 -1.265614016
[56] -1.116453030 0.522454997 -0.114228579 -2.264133608 -1.471310938
[61] 0.440491919 -0.728896925 -0.096097470 -1.014934164 -0.912799097
[66] 0.177770958 -2.179146720 0.094866431 0.248342640 -1.166252501
[71] 0.098756960 0.546022812 1.718025514 0.199593254 -0.387365371
[76] -0.727912583 0.264770469 -1.024829837 2.086007621 -0.970853230
[81] -0.294379037 0.589846201 -0.861696359 -0.723448277 -1.754459647
[86] -0.960392345 1.139827255 -1.191296216 0.400363951 -0.467328446
[91] 0.383458494 -0.333637914 -1.387669655 0.568515295 0.613229947
[96] -0.521050783 -0.852254981 -0.185576363 -0.520125443 0.402873071
> rowSums(tmp2)
[1] 1.268656816 -1.390924920 -0.095787611 -0.299043983 0.029618136
[6] -0.127087322 -0.074288563 -1.612409717 -0.462238369 -0.712800230
[11] 0.626164353 2.120442285 0.585654750 0.827579860 -1.304491394
[16] 0.884779691 -0.761047932 -0.444865622 0.227676281 0.007179428
[21] -0.509941644 -0.263039050 1.862931760 0.008842624 0.321902244
[26] 0.008534058 0.587884538 1.121518054 -1.809589241 0.351236167
[31] 1.246945355 0.946463709 0.205562918 -1.004508958 0.300687120
[36] 0.217996390 0.349889166 0.035803698 1.142626755 -0.658011835
[41] -0.241704010 -0.770561660 -0.852601828 0.469394916 0.834106828
[46] 0.342531117 0.874527093 -0.315187279 0.359189619 -0.145479408
[51] 1.434143401 1.021796070 -0.183935589 0.666162656 -1.265614016
[56] -1.116453030 0.522454997 -0.114228579 -2.264133608 -1.471310938
[61] 0.440491919 -0.728896925 -0.096097470 -1.014934164 -0.912799097
[66] 0.177770958 -2.179146720 0.094866431 0.248342640 -1.166252501
[71] 0.098756960 0.546022812 1.718025514 0.199593254 -0.387365371
[76] -0.727912583 0.264770469 -1.024829837 2.086007621 -0.970853230
[81] -0.294379037 0.589846201 -0.861696359 -0.723448277 -1.754459647
[86] -0.960392345 1.139827255 -1.191296216 0.400363951 -0.467328446
[91] 0.383458494 -0.333637914 -1.387669655 0.568515295 0.613229947
[96] -0.521050783 -0.852254981 -0.185576363 -0.520125443 0.402873071
> 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] 1.268656816 -1.390924920 -0.095787611 -0.299043983 0.029618136
[6] -0.127087322 -0.074288563 -1.612409717 -0.462238369 -0.712800230
[11] 0.626164353 2.120442285 0.585654750 0.827579860 -1.304491394
[16] 0.884779691 -0.761047932 -0.444865622 0.227676281 0.007179428
[21] -0.509941644 -0.263039050 1.862931760 0.008842624 0.321902244
[26] 0.008534058 0.587884538 1.121518054 -1.809589241 0.351236167
[31] 1.246945355 0.946463709 0.205562918 -1.004508958 0.300687120
[36] 0.217996390 0.349889166 0.035803698 1.142626755 -0.658011835
[41] -0.241704010 -0.770561660 -0.852601828 0.469394916 0.834106828
[46] 0.342531117 0.874527093 -0.315187279 0.359189619 -0.145479408
[51] 1.434143401 1.021796070 -0.183935589 0.666162656 -1.265614016
[56] -1.116453030 0.522454997 -0.114228579 -2.264133608 -1.471310938
[61] 0.440491919 -0.728896925 -0.096097470 -1.014934164 -0.912799097
[66] 0.177770958 -2.179146720 0.094866431 0.248342640 -1.166252501
[71] 0.098756960 0.546022812 1.718025514 0.199593254 -0.387365371
[76] -0.727912583 0.264770469 -1.024829837 2.086007621 -0.970853230
[81] -0.294379037 0.589846201 -0.861696359 -0.723448277 -1.754459647
[86] -0.960392345 1.139827255 -1.191296216 0.400363951 -0.467328446
[91] 0.383458494 -0.333637914 -1.387669655 0.568515295 0.613229947
[96] -0.521050783 -0.852254981 -0.185576363 -0.520125443 0.402873071
> rowMin(tmp2)
[1] 1.268656816 -1.390924920 -0.095787611 -0.299043983 0.029618136
[6] -0.127087322 -0.074288563 -1.612409717 -0.462238369 -0.712800230
[11] 0.626164353 2.120442285 0.585654750 0.827579860 -1.304491394
[16] 0.884779691 -0.761047932 -0.444865622 0.227676281 0.007179428
[21] -0.509941644 -0.263039050 1.862931760 0.008842624 0.321902244
[26] 0.008534058 0.587884538 1.121518054 -1.809589241 0.351236167
[31] 1.246945355 0.946463709 0.205562918 -1.004508958 0.300687120
[36] 0.217996390 0.349889166 0.035803698 1.142626755 -0.658011835
[41] -0.241704010 -0.770561660 -0.852601828 0.469394916 0.834106828
[46] 0.342531117 0.874527093 -0.315187279 0.359189619 -0.145479408
[51] 1.434143401 1.021796070 -0.183935589 0.666162656 -1.265614016
[56] -1.116453030 0.522454997 -0.114228579 -2.264133608 -1.471310938
[61] 0.440491919 -0.728896925 -0.096097470 -1.014934164 -0.912799097
[66] 0.177770958 -2.179146720 0.094866431 0.248342640 -1.166252501
[71] 0.098756960 0.546022812 1.718025514 0.199593254 -0.387365371
[76] -0.727912583 0.264770469 -1.024829837 2.086007621 -0.970853230
[81] -0.294379037 0.589846201 -0.861696359 -0.723448277 -1.754459647
[86] -0.960392345 1.139827255 -1.191296216 0.400363951 -0.467328446
[91] 0.383458494 -0.333637914 -1.387669655 0.568515295 0.613229947
[96] -0.521050783 -0.852254981 -0.185576363 -0.520125443 0.402873071
>
> colMeans(tmp2)
[1] -0.07750044
> colSums(tmp2)
[1] -7.750044
> colVars(tmp2)
[1] 0.8060876
> colSd(tmp2)
[1] 0.8978238
> colMax(tmp2)
[1] 2.120442
> colMin(tmp2)
[1] -2.264134
> colMedians(tmp2)
[1] -0.03355457
> colRanges(tmp2)
[,1]
[1,] -2.264134
[2,] 2.120442
>
> 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] -1.6456674 -3.4446176 -1.7368212 -0.4723140 0.3845706 -2.3143429
[7] -0.1816999 -4.2390209 -1.1280353 -1.4688029
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.0520708
[2,] -0.6454733
[3,] -0.2529771
[4,] 0.1076333
[5,] 1.1063707
>
> rowApply(tmp,sum)
[1] 7.649334 -3.183626 -3.742161 -3.913134 -1.184989 2.831605 3.202332
[8] -2.169501 -6.892276 -8.844335
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 2 4 10 2 3 6 4 5 7 5
[2,] 5 2 9 4 2 5 9 10 4 1
[3,] 8 10 4 6 8 3 2 4 2 6
[4,] 4 3 8 7 9 4 7 1 8 7
[5,] 1 7 5 5 4 9 6 9 10 3
[6,] 10 8 1 10 5 2 5 8 1 4
[7,] 7 9 3 9 1 7 3 7 6 10
[8,] 9 5 6 1 6 10 1 2 5 2
[9,] 6 6 2 8 7 1 10 6 3 9
[10,] 3 1 7 3 10 8 8 3 9 8
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -3.6271936 -1.6183987 -1.5436156 -1.1066252 -1.9760401 4.2589812
[7] 0.5475327 1.6514194 -1.2309337 2.3752275 -3.2228599 -2.7917491
[13] 0.5575329 2.3537466 0.5781374 -2.3680252 -0.5306779 -4.9074513
[19] 2.3296889 1.7570264
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.4957398
[2,] -0.6271352
[3,] -0.4966870
[4,] -0.1808885
[5,] 0.1732569
>
> rowApply(tmp,sum)
[1] -0.8246598 -6.6763798 4.4638112 -1.3954921 -4.0815569
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 7 1 12 8 10
[2,] 10 3 7 20 4
[3,] 5 17 5 6 13
[4,] 2 2 17 13 18
[5,] 15 6 1 14 12
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.6271352 -0.2501577 -0.67863374 -1.3019025 0.01093465 1.3128664
[2,] -2.4957398 -1.4468215 0.34947646 -2.1050024 -0.74942605 -0.3349452
[3,] 0.1732569 -0.3123746 -0.45872877 1.1038115 -1.61687627 2.4883229
[4,] -0.1808885 1.3582901 -0.72484550 0.2984810 0.53094596 0.6798873
[5,] -0.4966870 -0.9673350 -0.03088404 0.8979872 -0.15161843 0.1128499
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.2379070 -0.5018303 -0.197288266 -0.1057811 -1.2113348 -0.4797814
[2,] -0.1063682 0.1877496 0.033814506 1.3085590 0.5423861 -0.1716227
[3,] 1.4108020 0.6814001 -0.007733528 -0.5467122 -0.8003587 -1.2249058
[4,] 0.0641603 0.7914579 0.093439985 0.7002933 -0.7445336 0.2892767
[5,] -0.5831544 0.4926422 -1.153166408 1.0188684 -1.0090189 -1.2047158
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 1.9376952 0.6043372 -0.84281021 -0.2189583 -0.6424224 -1.55562062
[2,] -0.2739715 0.7939149 -0.01133684 -0.4175748 -0.9197784 -1.01710689
[3,] -0.2978233 1.0676300 0.62868079 0.5560627 -0.3255402 -0.09905117
[4,] -0.3030590 -1.0924497 1.14207907 -1.6146379 1.1756400 -1.28646235
[5,] -0.5053084 0.9803142 -0.33847542 -0.6729169 0.1814231 -0.94921025
[,19] [,20]
[1,] 0.868160370 3.29290996
[2,] 0.008540196 0.14887383
[3,] 1.978194343 0.06575471
[4,] 0.008030879 -2.58059804
[5,] -0.533236887 0.83008592
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.17-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-3.17-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 654 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 566 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.17-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 0.609963 -0.4388923 -0.7750819 0.3856342 0.04678866 -1.640141 1.63575
col8 col9 col10 col11 col12 col13 col14
row1 0.005836417 1.298982 -1.33843 1.295751 -0.1707335 1.092055 -1.363098
col15 col16 col17 col18 col19 col20
row1 0.9268093 -0.3132005 0.3409242 -0.4688913 -1.171238 1.4239
> tmp[,"col10"]
col10
row1 -1.3384302
row2 -0.7366876
row3 -1.3062448
row4 -0.4613174
row5 0.1736010
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 0.609963 -0.4388923 -0.7750819 0.3856342 0.04678866 -1.6401408 1.6357502
row5 1.052255 -0.7220679 0.1477517 -0.8422070 0.46067436 0.3236469 0.3444297
col8 col9 col10 col11 col12 col13 col14
row1 0.005836417 1.298982 -1.338430 1.295751 -0.1707335 1.0920550 -1.363098
row5 0.009633161 1.226547 0.173601 0.459570 -0.4245461 0.1140752 -1.246382
col15 col16 col17 col18 col19 col20
row1 0.9268093 -0.3132005 0.3409242 -0.4688913 -1.171238 1.42390029
row5 -0.2924145 1.5001940 1.0113470 -0.8587642 1.631911 -0.09825657
> tmp[,c("col6","col20")]
col6 col20
row1 -1.6401408 1.42390029
row2 0.9157547 0.33757703
row3 -2.0558971 -0.17328685
row4 -1.9838960 -0.19492817
row5 0.3236469 -0.09825657
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -1.6401408 1.42390029
row5 0.3236469 -0.09825657
>
>
>
>
> 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 49.29271 50.49018 50.38666 49.64038 49.14515 104.6431 49.44578 50.06264
col9 col10 col11 col12 col13 col14 col15 col16
row1 47.13647 48.11571 51.1861 48.68042 50.97096 50.54216 48.87737 49.88208
col17 col18 col19 col20
row1 50.74789 49.35403 48.61159 105.0315
> tmp[,"col10"]
col10
row1 48.11571
row2 29.40554
row3 28.56009
row4 28.53449
row5 49.04299
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.29271 50.49018 50.38666 49.64038 49.14515 104.6431 49.44578 50.06264
row5 48.86698 50.02211 48.55588 48.39798 50.55233 104.9853 49.83172 51.37121
col9 col10 col11 col12 col13 col14 col15 col16
row1 47.13647 48.11571 51.18610 48.68042 50.97096 50.54216 48.87737 49.88208
row5 49.32713 49.04299 49.05945 49.63591 50.56970 50.23605 49.72538 52.16110
col17 col18 col19 col20
row1 50.74789 49.35403 48.61159 105.0315
row5 50.99531 47.76930 50.44848 104.1235
> tmp[,c("col6","col20")]
col6 col20
row1 104.64309 105.03153
row2 74.20050 75.41714
row3 74.36119 74.61710
row4 75.87356 74.07451
row5 104.98529 104.12346
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.6431 105.0315
row5 104.9853 104.1235
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.6431 105.0315
row5 104.9853 104.1235
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.9828532
[2,] 0.4194113
[3,] -1.8437878
[4,] 0.4528811
[5,] 0.1797943
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.0379311 0.7989470
[2,] 0.5825871 0.6993458
[3,] -0.1726010 -0.8217381
[4,] -0.7249292 0.1063538
[5,] -1.3868063 0.1531594
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 0.62797361 1.0131070
[2,] 0.64871852 -1.1380189
[3,] -0.09427447 2.1515134
[4,] 0.72650794 -0.7195736
[5,] 0.11862215 0.7338416
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 0.6279736
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 0.6279736
[2,] 0.6487185
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6]
row3 -2.1204816 -0.7061544 -0.004360764 0.7624703 -0.5605193 0.8655715
row1 0.7749622 2.6927213 -0.836643149 0.3134319 -1.5231550 -0.6435410
[,7] [,8] [,9] [,10] [,11] [,12]
row3 -0.8096515 0.6546369 0.08925178 1.11295312 -0.3211285 -2.061164
row1 -0.4671704 0.7652350 -0.72139368 -0.07663114 -0.2060075 -1.346471
[,13] [,14] [,15] [,16] [,17] [,18] [,19]
row3 0.1661993 0.9914731 -1.1587538 -0.7713248 0.522802 -0.2846216 1.564979
row1 -1.0072763 0.4419884 0.5733011 -1.2899423 1.166526 0.2915814 -1.163148
[,20]
row3 0.5756144
row1 1.6869665
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 1.199533 0.164269 0.1834371 -0.196082 -0.1883747 -0.5118729 0.9898146
[,8] [,9] [,10]
row2 0.7704773 0.7980719 0.3114465
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.1728081 -2.66557 0.6354741 0.3009243 0.5692742 0.6891881 0.4885372
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 1.920071 0.9418263 1.029774 -0.08488234 -1.563823 -0.1759639 -0.5537607
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.563136 -0.5008974 -0.9558889 -0.2228845 1.851054 -0.5331445
>
>
> 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: 0xaaaae1d550d0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM2814ee68e653d2"
[2] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM2814ee4b6cb9d"
[3] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM2814ee3de4cc7c"
[4] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM2814ee68fa555d"
[5] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM2814ee4cc249fc"
[6] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM2814ee7ae80da9"
[7] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM2814ee67fc178a"
[8] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM2814ee109de0de"
[9] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM2814ee5ef4865d"
[10] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM2814ee1bafc133"
[11] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM2814ee7a40de2e"
[12] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM2814ee3e479ea7"
[13] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM2814ee55097bde"
[14] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM2814ee4bffdea4"
[15] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM2814ee4338dfba"
>
>
> ### 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: 0xaaaae2f5fde0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0xaaaae2f5fde0>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0xaaaae2f5fde0>
> rowMedians(tmp)
[1] -0.126630363 0.077495606 0.088357017 0.229853170 0.279349408
[6] -0.235238669 0.303521068 0.037173031 0.018665716 0.411129785
[11] 0.101464775 0.778102007 -0.795153113 -0.160354159 -0.620874663
[16] -0.205135694 -0.041982390 -0.129326635 0.022410920 0.824771616
[21] 0.197336307 -0.597275363 -0.343191317 0.285395227 0.113352795
[26] -0.229249983 0.404258946 -0.405508146 0.144323260 0.079158690
[31] 0.655037682 0.457633387 0.207859128 -0.061954042 -0.191615426
[36] 0.032982851 -0.091298449 0.041282864 -0.637170270 0.782884075
[41] 0.124239804 1.070122500 0.347949682 0.223927114 0.159428847
[46] -0.151023490 0.017158023 0.226065376 0.572783286 -0.018222573
[51] -0.186971969 0.140106937 0.022222388 0.008819806 -0.293726366
[56] 0.031277105 -0.038585493 0.173701904 -0.557198365 0.218845387
[61] 0.485377829 0.121466834 -0.441806540 0.022411332 -0.710801500
[66] -0.302327464 0.058767128 0.135456855 -0.311104010 -0.261449379
[71] -0.544866645 -0.227345556 0.092378123 0.353848267 -0.181588996
[76] 0.342629758 -0.115462437 0.386886756 -0.114003908 -0.446105555
[81] -0.239984029 -0.097558318 0.174778200 0.189620832 -0.078067396
[86] 0.317379903 0.127397812 -0.004854447 -0.328368331 -0.111934025
[91] -0.366609598 -0.216340706 -0.393177930 0.124021515 -0.153200884
[96] -0.471345671 0.332795379 -0.418713227 0.915468079 0.133867366
[101] -0.518164406 0.102208752 -0.557012553 0.464382594 0.154441754
[106] -0.915464953 -0.317857154 -0.108618202 -0.498855160 -0.009407520
[111] 0.029211124 -0.093238163 -0.111559464 0.123068696 -0.450808711
[116] -0.475482623 -0.239170837 0.171674873 -0.351233964 -0.485505034
[121] 0.366932618 0.659284444 -0.057256616 0.134383390 -0.293687704
[126] -0.133606321 -0.306309712 -0.240906331 -0.035127580 0.270784381
[131] 0.574479863 -0.148533134 0.294987332 -0.660122844 -0.332664206
[136] -0.618439572 -0.276581478 -0.064784518 -0.223132557 -0.261974965
[141] -0.287240426 -0.173875556 -0.241137839 0.083515125 -0.314301944
[146] -0.264930451 0.359110860 0.422528209 -0.420785435 -0.026277323
[151] -0.004511701 0.418301056 0.440090505 0.047786217 -0.711541498
[156] -0.187988312 0.064724826 -0.202383884 -0.041823335 0.162968999
[161] 0.044306377 -0.268209681 -0.203025350 0.646543200 0.157567970
[166] -0.594316270 -0.017497293 0.065779469 -0.082068519 0.279954996
[171] -0.443355360 0.022689113 0.467394000 -0.554582725 0.020741412
[176] -0.217373232 0.268392435 -0.723870610 -0.376833359 0.158511739
[181] -0.002612272 -0.266285294 0.349227549 -0.074786755 -0.270852696
[186] -0.293978870 0.074994234 -0.191132638 0.082341848 -0.075972408
[191] 0.046231707 0.013549083 -0.849586020 -0.138425213 0.413057183
[196] -0.448842458 -0.108985669 -0.035829641 0.386983264 -0.443758309
[201] -0.109913187 0.176254487 -0.012546354 0.159122785 -0.114608729
[206] -0.566446365 0.330780494 -0.251006696 -0.311476485 -0.191226084
[211] 0.206057572 -0.095860690 0.208312007 -0.208622474 -0.560313541
[216] 0.687831819 -0.047499240 0.597128886 -0.272252672 0.019421718
[221] 0.065052431 0.014847734 0.126769578 -0.441415192 -0.473793650
[226] -0.018417157 -0.302704211 0.060459203 -0.408322791 0.386762582
>
> proc.time()
user system elapsed
1.905 1.409 3.336
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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: 0xaaaae7763910>
> .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: 0xaaaae7763910>
> .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: 0xaaaae7763910>
> .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: 0xaaaae7763910>
> 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: 0xaaaae7f242a0>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaae7f242a0>
> .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: 0xaaaae7f242a0>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaae7f242a0>
> .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: 0xaaaae7f242a0>
> 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: 0xaaaae7711df0>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaae7711df0>
> .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: 0xaaaae7711df0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0xaaaae7711df0>
> .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: 0xaaaae7711df0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0xaaaae7711df0>
> .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: 0xaaaae7711df0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0xaaaae7711df0>
> .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: 0xaaaae7711df0>
> 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: 0xaaaae7f8f3a0>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0xaaaae7f8f3a0>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaae7f8f3a0>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaae7f8f3a0>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile28155c2549715e" "BufferedMatrixFile28155c54073ffb"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile28155c2549715e" "BufferedMatrixFile28155c54073ffb"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaae98c89b0>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaae98c89b0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0xaaaae98c89b0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0xaaaae98c89b0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0xaaaae98c89b0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0xaaaae98c89b0>
> .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: 0xaaaae939f010>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaae939f010>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0xaaaae939f010>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0xaaaae939f010>
> 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: 0xaaaae98d4530>
> .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: 0xaaaae98d4530>
> rm(P)
>
> proc.time()
user system elapsed
0.324 0.055 0.363
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
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> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.334 0.049 0.368