puma 3.13.0
Xuejun Liu
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/puma | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings puma_3.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/puma.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (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 ‘3.13.0’
* 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 ... [19s/20s] OK
* 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 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’
clusterApplyLBDots : submit: no visible global function definition for
‘sendCall’
clusterApplyLBDots: no visible global function definition for
‘recvOneResult’
compareLimmapumaDE: no visible global function definition for
‘vennDiagram’
gmhta: no visible global function definition for ‘clusterEvalQ’
gmhta: no visible global function definition for ‘clusterApplyLB’
gmhta: no visible global function definition for ‘stopCluster’
gmoExon: no visible global function definition for ‘clusterEvalQ’
gmoExon: no visible global function definition for ‘clusterApplyLB’
gmoExon: no visible global function definition for ‘stopCluster’
igmoExon: no visible global function definition for ‘clusterEvalQ’
igmoExon: no visible global function definition for ‘clusterApplyLB’
igmoExon: no visible global function definition for ‘stopCluster’
plotErrorBars: no visible global function definition for ‘even’
plotErrorBars: no visible global function definition for ‘odd’
plotROC: no visible global function definition for ‘prediction’
plotROC: no visible global function definition for ‘performance’
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’
Undefined global functions or variables:
clusterApplyLB clusterEvalQ contrasts.fit description eBayes even
getMPIcluster lmFit makeCluster odd performance prediction
recvOneResult sendCall stopCluster vennDiagram
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [198s/198s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
puma-package 43.311 0.020 43.381
pumaClustii 28.759 0.004 28.793
pumaDE 28.027 0.036 28.086
hcomb 22.482 0.056 22.564
pumaComb 15.195 0.016 15.227
pumaCombImproved 14.431 0.032 14.478
DEResult-class 13.491 0.008 13.516
plot-methods 6.335 0.004 6.346
pumaPCA 6.101 0.004 6.112
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/puma.Rcheck/00check.log’
for details.
* installing *source* package ‘puma’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c PMmultimgmos.c -o PMmultimgmos.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c cregistration.c -o cregistration.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c donlp2.c -o donlp2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c gme.c -o gme.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ipplr_c.c -o ipplr_c.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c multimgmos.c -o multimgmos.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c newx.c -o newx.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c pplr_c.c -o pplr_c.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c pumaclust_c.c -o pumaclust_c.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c pumaclustii_c.c -o pumaclustii_c.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c user_eval.c -o user_eval.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/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 -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/puma.Rcheck/puma/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (puma)