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CHECK report for Biobase on celaya2

This page was generated on 2019-10-16 12:44:29 -0400 (Wed, 16 Oct 2019).

Package 139/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biobase 2.44.0
Bioconductor Package Maintainer
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/Biobase
Branch: RELEASE_3_9
Last Commit: bde2077
Last Changed Date: 2019-05-02 11:53:01 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Biobase
Version: 2.44.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Biobase.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Biobase_2.44.0.tar.gz
StartedAt: 2019-10-16 00:52:27 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:54:44 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 136.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Biobase.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Biobase.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Biobase_2.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Biobase.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biobase/DESCRIPTION’ ... OK
* this is package ‘Biobase’ version ‘2.44.0’
* 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 ‘Biobase’ can be installed ... OK
* 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 ... OK
* 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 contents of ‘data’ directory ... WARNING
Output for data("sample.eSet", package = "Biobase"):
  No dataset created in 'envir'
Output for data("sample.exprSet.1", package = "Biobase"):
  No dataset created in 'envir'
Output for data("sample.exprSet", package = "Biobase"):
  No dataset created in 'envir'
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
  Running ‘test-rowMedians.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/Biobase.Rcheck/00check.log’
for details.



Installation output

Biobase.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Biobase
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Biobase’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Rinit.c -o Rinit.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c anyMissing.c -o anyMissing.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c envir.c -o envir.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c matchpt.c -o matchpt.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c rowMedians.c -o rowMedians.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c sublist_extract.c -o sublist_extract.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Biobase/00new/Biobase/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 (Biobase)

Tests output

Biobase.Rcheck/tests/test-all.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> BiocGenerics:::testPackage("Biobase")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.



RUNIT TEST PROTOCOL -- Wed Oct 16 00:53:56 2019 
*********************************************** 
Number of test functions: 101 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Biobase RUnit Tests - 101 test functions, 0 errors, 0 failures
Number of test functions: 101 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 20.038   0.670  20.683 

Biobase.Rcheck/tests/test-rowMedians.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(Biobase)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> set.seed(1)
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Consistency checks
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> 
> # rowMedians() by rowQ()
> rowMedians2 <- function(imat) {
+   nr <- ncol(imat)
+   half <- (nr + 1)/2
+   if (nr%%2 == 1) {
+     return(rowQ(imat, half))
+   } else {
+     return((rowQ(imat, half) + rowQ(imat, half+1))/2)
+   }
+ }
> 
> cat("Consistency checks:\n")
Consistency checks:
> set.seed(1)
> for (kk in 1:20) {
+   cat("Random test #", kk, "\n", sep="")
+ 
+   # Simulate data in a matrix of any shape
+   nrow <- sample(2000, size=1)
+   ncol <- sample(2000, size=1)
+   x <- rnorm(nrow*ncol)
+   dim(x) <- c(nrow, ncol)
+ 
+   # Add NAs?
+   nas <- sample(c(TRUE,FALSE), size=1)
+   if (nas) {
+     nna <- sample(nrow*ncol, size=1)
+     x[sample(length(x), size=nna)] <- NA
+   }
+ 
+   na.rm <- nas
+   t1 <- system.time({
+     y1 <- rowMedians(x, na.rm=na.rm)
+   })
+   t2 <- system.time({
+     y2 <- apply(x, MARGIN=1, FUN=median, na.rm=na.rm)
+   })
+   # When all values of 'y2' are NA, 'y2' is logical
+   if (is.logical(y2)) y2 <- as.double(y2)
+   stopifnot(all.equal(y1,y2))
+   cat(sprintf("rowMedians()/apply(): %.3g\n", (t1/t2)[3]))
+ 
+   if (!nas) {
+     t3 <- system.time({
+       y3 <- rowMedians2(x)
+     })
+     stopifnot(all.equal(y1,y3))
+     cat(sprintf("rowMedians()/rowMedians2(): %.3g\n", (t1/t3)[3]))
+   }
+ }
Random test #1
rowMedians()/apply(): 0.354
Random test #2
rowMedians()/apply(): 0.137
rowMedians()/rowMedians2(): 0.514
Random test #3
rowMedians()/apply(): 0.0192
Random test #4
rowMedians()/apply(): 0.286
rowMedians()/rowMedians2(): 0.386
Random test #5
rowMedians()/apply(): 0.366
rowMedians()/rowMedians2(): 0.422
Random test #6
rowMedians()/apply(): 0.451
rowMedians()/rowMedians2(): 0.604
Random test #7
rowMedians()/apply(): 0.317
Random test #8
rowMedians()/apply(): 0.00585
rowMedians()/rowMedians2(): Inf
Random test #9
rowMedians()/apply(): 0.103
Random test #10
rowMedians()/apply(): 0.0827
Random test #11
rowMedians()/apply(): 0.136
Random test #12
rowMedians()/apply(): 0.231
Random test #13
rowMedians()/apply(): 0.296
rowMedians()/rowMedians2(): 1
Random test #14
rowMedians()/apply(): 0.256
Random test #15
rowMedians()/apply(): 0.404
Random test #16
rowMedians()/apply(): 0.137
rowMedians()/rowMedians2(): 0.471
Random test #17
rowMedians()/apply(): 0.62
Random test #18
rowMedians()/apply(): 0.076
rowMedians()/rowMedians2(): 0.826
Random test #19
rowMedians()/apply(): 0.536
rowMedians()/rowMedians2(): 0.977
Random test #20
rowMedians()/apply(): 0.4
rowMedians()/rowMedians2(): 0.439
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Benchmarking
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> cat("Benchmarking:\n")
Benchmarking:
> 
> # Simulate data in a matrix of any shape
> nrow <- 1000
> ncol <- 1000
> x <- rnorm(nrow*ncol)
> dim(x) <- c(nrow, ncol)
> 
> gc()
          used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells  574411 30.7    1142760 61.1         NA  1022710 54.7
Vcells 2050399 15.7   12255594 93.6      57344 12276796 93.7
> t0 <- system.time({
+   for (rr in 1:20)
+     y0 <- apply(x, MARGIN=1, FUN=median, na.rm=FALSE)
+ })
> gc()
          used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells  574428 30.7    1142760 61.1         NA  1142760 61.1
Vcells 2051417 15.7   12255594 93.6      57344 12276796 93.7
> t1 <- system.time({
+   for (rr in 1:20)
+     y1 <- rowMedians(x, na.rm=FALSE)
+ })
> gc()
          used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells  574428 30.7    1142760 61.1         NA  1142760 61.1
Vcells 2050542 15.7   12255594 93.6      57344 12276796 93.7
> stopifnot(all.equal(y0,y1))
> cat(sprintf("rowMedians()/apply(): %.3g\n", (t1/t0)[3]))
rowMedians()/apply(): 0.307
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Consistency checks
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> cat("Consistency checks without NAs:\n")
Consistency checks without NAs:
> for (kk in 1:20) {
+   cat("Random test #", kk, "\n", sep="")
+ 
+   # Simulate data in a matrix of any shape
+   nrow <- sample(1000, size=1)
+   ncol <- sample(1000, size=1)
+   x <- rnorm(nrow*ncol)
+   dim(x) <- c(nrow, ncol)
+ 
+   t0 <- system.time({
+     y0 <- apply(x, MARGIN=1, FUN=median, na.rm=FALSE)
+   })
+   t1 <- system.time({
+     y1 <- rowMedians(x, na.rm=FALSE)
+   })
+   stopifnot(all.equal(y0,y1))
+ } # for (kk in ...)
Random test #1
Random test #2
Random test #3
Random test #4
Random test #5
Random test #6
Random test #7
Random test #8
Random test #9
Random test #10
Random test #11
Random test #12
Random test #13
Random test #14
Random test #15
Random test #16
Random test #17
Random test #18
Random test #19
Random test #20
> 
> 
> 
> cat("Consistency checks with NAs:\n")
Consistency checks with NAs:
> for (kk in 1:20) {
+   cat("Random test #", kk, "\n", sep="")
+ 
+   # Simulate data in a matrix of any shape
+   nrow <- sample(1000, size=1)
+   ncol <- sample(1000, size=1)
+   x <- rnorm(nrow*ncol)
+   dim(x) <- c(nrow, ncol)
+ 
+   # Add NAs
+   nna <- sample(nrow*ncol-1, size=1)
+   x[sample(length(x), size=nna)] <- NA
+ 
+   t0 <- system.time({
+     y0 <- apply(x, MARGIN=1, FUN=median, na.rm=TRUE)
+     y0[is.na(y0)] <- NA
+   })
+   t1 <- system.time({
+     y1 <- rowMedians(x, na.rm=TRUE)
+   })
+   stopifnot(all.equal(y0,y1))
+ } # for (kk in ...)
Random test #1
Random test #2
Random test #3
Random test #4
Random test #5
Random test #6
Random test #7
Random test #8
Random test #9
Random test #10
Random test #11
Random test #12
Random test #13
Random test #14
Random test #15
Random test #16
Random test #17
Random test #18
Random test #19
Random test #20
> 
> proc.time()
   user  system elapsed 
 33.729   1.623  36.780 

Example timings

Biobase.Rcheck/Biobase-Ex.timings

nameusersystemelapsed
Aggregate0.0110.0010.011
ScalarObject-class0.0180.0000.018
addVig2Menu0.0000.0000.001
anyMissing0.0030.0000.003
cache0.0050.0020.008
channel0.3880.0640.452
channelNames0.0650.0000.065
class.AnnotatedDataFrame0.0470.0010.048
class.ExpressionSet0.2370.0170.254
class.MIAxE0.0200.0010.021
class.MultiSet0.0250.0000.026
class.NChannelSet0.1420.0020.144
class.Versioned0.0620.0010.063
class.VersionedBiobase0.0300.0010.032
class.Versions0.0180.0010.019
class.VersionsNull0.0020.0010.002
class.container0.0040.0000.004
class.eSet0.1280.0020.131
classVersion0.0070.0010.008
contents0.0020.0010.003
copyEnv0.0010.0000.001
copySubstitute0.0190.0110.029
createPackage0.0080.0050.015
data.aaMap0.0030.0020.006
data.geneData0.0440.0080.051
data.reporter0.0030.0020.005
data.sample.ExpressionSet0.0190.0160.035
data.sample.MultiSet0.0070.0110.018
dumpPackTxt0.0010.0010.004
esApply2.0740.0302.105
getPkgVigs0.0150.0040.021
isCurrent0.0320.0010.033
isUnique0.0010.0010.001
isVersioned0.0140.0010.014
lcSuffix0.0020.0000.004
listLen0.0010.0000.002
makeDataPackage0.0760.0180.094
matchpt0.0080.0010.009
multiassign0.0020.0000.002
note000
openPDF0.0000.0010.001
openVignette0.0010.0010.000
package.version0.0010.0000.002
read.AnnotatedDataFrame0.0140.0020.017
read.MIAME0.0010.0010.003
readExpressionSet0.1180.0110.129
reverseSplit0.0010.0000.002
rowMedians0.0670.0120.079
rowQ0.0270.0230.050
selectChannels0.0690.0040.071
selectSome0.0010.0010.001
strbreak0.0020.0000.002
subListExtract0.8980.0570.955
testBioCConnection0.0040.0040.318
updateOldESet000
validMsg0.0000.0000.001