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This page was generated on 2022-01-17 13:08:12 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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

CHECK results for puma on machv2


To the developers/maintainers of the puma package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/puma.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1486/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
puma 3.36.0  (landing page)
Xuejun Liu
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/puma
git_branch: RELEASE_3_14
git_last_commit: 661a7da
git_last_commit_date: 2021-10-26 11:51:13 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: puma
Version: 3.36.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:puma.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings puma_3.36.0.tar.gz
StartedAt: 2022-01-16 16:43:36 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 16:50:56 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 439.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: puma.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:puma.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings puma_3.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/puma.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘puma/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘puma’ version ‘3.36.0’
* 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 ‘puma’ can be installed ... WARNING
Found the following significant warnings:
  pumaclust_c.c:181:24: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Users/biocbuild/bbs-3.14-bioc/meat/puma.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘oligoClasses’
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' calls in package code:
  ‘ROCR’ ‘limma’ ‘pumadata’ ‘snow’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' calls which should be '::':
  ‘affy:::mm’ ‘affy:::pm’ ‘affy:::probeNames’ ‘oligo:::mm’ ‘oligo:::pm’
  ‘oligo:::probeNames’ ‘oligo:::rma’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PMmmgmos: no visible binding for global variable ‘median’
PMmmgmos: no visible global function definition for ‘description’
calcAUC: no visible global function definition for ‘prediction’
calcAUC: no visible global function definition for ‘performance’
calculateLimma: no visible global function definition for ‘lmFit’
calculateLimma: no visible global function definition for
  ‘contrasts.fit’
calculateLimma: no visible global function definition for ‘eBayes’
calculateTtest : <anonymous>: no visible global function definition for
  ‘t.test’
clusterApplyLBDots : submit: no visible global function definition for
  ‘sendCall’
clusterApplyLBDots: no visible global function definition for
  ‘recvOneResult’
clusterNormE: no visible global function definition for ‘var’
clusterNormVar: no visible global function definition for ‘var’
compareLimmapumaDE: no visible global function definition for ‘pdf’
compareLimmapumaDE: no visible global function definition for ‘dev.off’
compareLimmapumaDE: no visible global function definition for ‘par’
compareLimmapumaDE: no visible global function definition for
  ‘vennDiagram’
createDesignMatrix: no visible global function definition for
  ‘model.matrix’
erfc: no visible global function definition for ‘pnorm’
gmhta: no visible global function definition for ‘clusterEvalQ’
gmhta: no visible global function definition for ‘data’
gmhta: no visible global function definition for ‘clusterApplyLB’
gmhta: no visible global function definition for ‘stopCluster’
gmhta: no visible binding for global variable ‘median’
gmoExon: no visible global function definition for ‘clusterEvalQ’
gmoExon: no visible global function definition for ‘data’
gmoExon: no visible global function definition for ‘clusterApplyLB’
gmoExon: no visible global function definition for ‘stopCluster’
gmoExon: no visible binding for global variable ‘median’
igmoExon: no visible global function definition for ‘clusterEvalQ’
igmoExon: no visible global function definition for ‘read.table’
igmoExon: no visible global function definition for ‘data’
igmoExon: no visible global function definition for ‘clusterApplyLB’
igmoExon: no visible global function definition for ‘stopCluster’
igmoExon: no visible binding for global variable ‘median’
just.mgmos: no visible binding for global variable ‘median’
just.mmgmos: no visible binding for global variable ‘median’
legend2: no visible global function definition for ‘par’
legend2: no visible global function definition for ‘xy.coords’
legend2 : rect2: no visible global function definition for ‘rect’
legend2 : segments2: no visible global function definition for
  ‘segments’
legend2 : points2: no visible global function definition for ‘points’
legend2 : text2: no visible global function definition for ‘text’
legend2: no visible global function definition for ‘strwidth’
legend2: no visible global function definition for ‘xinch’
legend2: no visible global function definition for ‘yinch’
legend2: no visible global function definition for ‘strheight’
matrixDistance: no visible global function definition for ‘dist’
mgmos: no visible binding for global variable ‘median’
mmgmos: no visible binding for global variable ‘median’
plot.pumaPCARes: no visible global function definition for ‘text’
plot.pumaPCARes: no visible global function definition for ‘legend’
plotErrorBars: no visible global function definition for ‘qnorm’
plotErrorBars: no visible global function definition for ‘par’
plotErrorBars: no visible global function definition for ‘even’
plotErrorBars: no visible global function definition for ‘odd’
plotErrorBars: no visible global function definition for ‘arrows’
plotErrorBars: no visible global function definition for ‘points’
plotErrorBars: no visible global function definition for ‘axis’
plotErrorBars: no visible global function definition for ‘title’
plotHistTwoClasses: no visible global function definition for ‘axis’
plotHistTwoClasses: no visible global function definition for ‘box’
plotROC: no visible global function definition for ‘prediction’
plotROC: no visible global function definition for ‘performance’
plotWhiskers: no visible global function definition for ‘segments’
plotWhiskers: no visible global function definition for ‘qnorm’
plotWhiskers: no visible global function definition for ‘points’
plotWhiskers: no visible global function definition for ‘abline’
pumaClust: no visible global function definition for ‘read.csv’
pumaClust: no visible global function definition for ‘kmeans’
pumaClust: no visible global function definition for ‘cov’
pumaClustii: no visible global function definition for ‘read.csv’
pumaClustii: no visible global function definition for ‘cov’
pumaComb: no visible global function definition for ‘getMPIcluster’
pumaComb: no visible global function definition for ‘makeCluster’
pumaComb: no visible global function definition for ‘clusterEvalQ’
pumaComb: no visible global function definition for ‘clusterApplyLB’
pumaCombImproved: no visible global function definition for
  ‘getMPIcluster’
pumaCombImproved: no visible global function definition for
  ‘makeCluster’
pumaCombImproved: no visible global function definition for
  ‘clusterEvalQ’
pumaCombImproved: no visible global function definition for
  ‘clusterApplyLB’
pumaFull: no visible global function definition for ‘pdf’
pumaFull: no visible global function definition for ‘par’
pumaFull: no visible global function definition for ‘prcomp’
pumaFull: no visible global function definition for ‘dev.off’
pumaNormalize: no visible binding for global variable ‘median’
pumaPCA: no visible global function definition for ‘prcomp’
pumaPCA: no visible global function definition for ‘rnorm’
pumaPCA: no visible global function definition for ‘optimise’
pumaPCA: no visible global function definition for ‘optim’
pumaPCA: no visible global function definition for ‘par’
pumaPCARemoveRedundancy: no visible global function definition for
  ‘dist’
write.reslts,DEResult: no visible global function definition for
  ‘write.table’
write.reslts,ExpressionSet: no visible global function definition for
  ‘write.table’
write.reslts,exprReslt: no visible global function definition for
  ‘write.table’
write.reslts,pumaPCARes: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  abline arrows axis box clusterApplyLB clusterEvalQ contrasts.fit cov
  data description dev.off dist eBayes even getMPIcluster kmeans legend
  lmFit makeCluster median model.matrix odd optim optimise par pdf
  performance pnorm points prcomp prediction qnorm read.csv read.table
  rect recvOneResult rnorm segments sendCall stopCluster strheight
  strwidth t.test text title var vennDiagram write.table xinch
  xy.coords yinch
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "xy.coords")
  importFrom("graphics", "abline", "arrows", "axis", "box", "legend",
             "par", "points", "rect", "segments", "strheight",
             "strwidth", "text", "title", "xinch", "yinch")
  importFrom("stats", "cov", "dist", "kmeans", "median", "model.matrix",
             "optim", "optimise", "pnorm", "prcomp", "qnorm", "rnorm",
             "t.test", "var")
  importFrom("utils", "data", "read.csv", "read.table", "write.table")
to your NAMESPACE file.
* 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
puma-package     55.297  1.622  56.967
pumaDE           38.475  1.231  39.880
pumaCombImproved 23.716  0.993  24.735
pumaComb         13.707  0.158  13.877
plot-methods     10.126  0.428  10.565
pumaPCA           9.397  0.297   9.701
pumaclust         5.579  0.018   5.610
* 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/puma.Rcheck/00check.log’
for details.



Installation output

puma.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL puma
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘puma’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c PMmultimgmos.c -o PMmultimgmos.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c cregistration.c -o cregistration.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c donlp2.c -o donlp2.o
donlp2.c:2034:1: warning: '/*' within block comment [-Wcomment]
/* **************************************************************************** */
^
donlp2.c:2707:1: warning: '/*' within block comment [-Wcomment]
/* inactive  
^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gme.c -o gme.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ipplr_c.c -o ipplr_c.o
ipplr_c.c:255:118: warning: '&&' within '||' [-Wlogical-op-parentheses]
                   while((fmaxn_ipplr(diff_mu1,in_param.conds)>in_param.eps)||(fmaxn_ipplr(diff_lamda,in_param.conds)>in_param.eps)&& (n<2000))
                                                                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
ipplr_c.c:255:118: note: place parentheses around the '&&' expression to silence this warning
                   while((fmaxn_ipplr(diff_mu1,in_param.conds)>in_param.eps)||(fmaxn_ipplr(diff_lamda,in_param.conds)>in_param.eps)&& (n<2000))
                                                                                                                                   ^
                                                                              (                                                               )
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c multimgmos.c -o multimgmos.o
multimgmos.c:893:95: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        double alphaii[MAX_NUM_COND]={0.0}, s1[MAX_NUM_COND]={0.0}, s2[MAX_NUM_PROBE][MAX_NUM_COND]={0.0}, c, d_mmgmos, t1, s3, s4;
                                                                                                     ^~~
                                                                                                     {  }
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c newx.c -o newx.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pplr_c.c -o pplr_c.o
pplr_c.c:185:65: warning: unused variable 'x_temp' [-Wunused-variable]
        double exp_c[MAX_NUM_REPLICATE], var_c[MAX_NUM_REPLICATE], x_temp[MAX_NUM_COND];
                                                                   ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pumaclust_c.c -o pumaclust_c.o
pumaclust_c.c:181:24: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
        while (foptold-fopt > abs(in_param.eps*fopt))
                              ^
pumaclust_c.c:181:24: note: use function 'fabs' instead
        while (foptold-fopt > abs(in_param.eps*fopt))
                              ^~~
                              fabs
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pumaclustii_c.c -o pumaclustii_c.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c user_eval.c -o user_eval.o
clang -mmacosx-version-min=10.13 -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 puma.so PMmultimgmos.o cregistration.o donlp2.o gme.o ipplr_c.o multimgmos.o newx.o pplr_c.o pumaclust_c.o pumaclustii_c.o user_eval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-puma/00new/puma/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘puma.Rnw’ using ‘UTF-8’ 
** 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 (puma)

Tests output


Example timings

puma.Rcheck/puma-Ex.timings

nameusersystemelapsed
DEResult-class0.0030.0010.003
PMmmgmos0.0010.0000.001
bcomb0.0000.0010.000
calcAUC000
calculateFC000
calculateLimma000
calculateTtest000
clusterNormE0.0000.0010.001
clusterNormVar000
createContrastMatrix0.0440.0030.047
createDesignMatrix0.1470.0050.152
erfc0.0010.0010.000
exprReslt-class0.0000.0010.001
gmhta0.0000.0010.001
gmoExon0.0000.0000.001
hcomb0.0000.0000.001
igmoExon0.0010.0000.001
legend20.0020.0000.002
license.puma0.0010.0010.002
matrixDistance0.0000.0010.000
mgmos0.0010.0010.001
mmgmos0.0000.0010.001
normalisation.gs0.0000.0010.000
numFP0.0010.0010.001
numOfFactorsToUse0.0000.0000.001
numTP0.0010.0000.002
orig_pplr0.0010.0000.001
plot-methods10.126 0.42810.565
plotErrorBars0.3990.0090.409
plotHistTwoClasses0.0140.0020.015
plotROC0.0010.0010.001
pplr0.2650.0260.293
puma-package55.297 1.62256.967
pumaClustii3.6050.0183.626
pumaComb13.707 0.15813.877
pumaCombImproved23.716 0.99324.735
pumaDE38.475 1.23139.880
pumaFull000
pumaNormalize0.3230.0080.331
pumaPCA9.3970.2979.701
pumaclust5.5790.0185.610
removeUninformativeFactors0.0580.0010.058