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BioC 2.14: CHECK report for maigesPack on zin2

This page was generated on 2014-10-08 08:48:17 -0700 (Wed, 08 Oct 2014).

Package 455/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maigesPack 1.28.1
Gustavo H. Esteves
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/maigesPack
Last Changed Rev: 94792 / Revision: 95116
Last Changed Date: 2014-10-01 11:03:27 -0700 (Wed, 01 Oct 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: maigesPack
Version: 1.28.1
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings maigesPack_1.28.1.tar.gz
StartedAt: 2014-10-08 00:48:10 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 00:50:35 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 145.7 seconds
RetCode: 0
Status:  OK 
CheckDir: maigesPack.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings maigesPack_1.28.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/maigesPack.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maigesPack/DESCRIPTION’ ... OK
* this is package ‘maigesPack’ version ‘1.28.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maigesPack’ can be installed ... [6s/7s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [66s/67s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
normScaleLimma  11.864  0.408  12.337
plot-methods     7.749  0.036   8.124
boxplot-methods  5.769  0.456   6.234
* 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/maigesPack.Rcheck/00check.log’
for details.

maigesPack.Rcheck/00install.out:

* installing *source* package ‘maigesPack’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Minfo.c -o Minfo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c bootstrapT.c -o bootstrapT.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c register.c -o register.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c robustCorr.c -o robustCorr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c stats.c -o stats.o
gcc -std=gnu99 -shared -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/meat/maigesPack.Rcheck/maigesPack/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (maigesPack)

maigesPack.Rcheck/maigesPack-Ex.timings:

nameusersystemelapsed
MI0.0040.0040.005
activeMod2.0480.0082.059
activeModScoreHTML1.0160.0041.020
activeNet3.8000.0083.814
activeNetScoreHTML3.8040.0003.820
addGeneGrps000
addPaths0.0040.0000.001
bootstrapCor0.0360.0000.036
bootstrapMI0.2480.0000.246
bootstrapT0.0000.0040.003
boxplot-methods5.7690.4566.234
bracketMethods0.1840.0040.186
calcA0.1760.0640.240
calcW0.1880.0600.247
classifyKNN0.2160.0040.217
classifyKNNsc0.2680.0000.269
classifyLDA0.8520.0000.855
classifyLDAsc1.6400.0001.644
classifySVM0.4760.0160.490
classifySVMsc0.7760.0120.788
coerce-methods0.1080.0120.121
compCorr0.0040.0000.000
createMaigesRaw0.2440.0000.244
deGenes2by2BootT0.4360.0040.440
deGenes2by2Ttest0.2680.0000.266
deGenes2by2Wilcox0.2560.0000.254
deGenesANOVA0.1960.0040.198
designANOVA0.1680.0040.175
dim-methods0.0640.0000.065
getLabels0.0760.0000.077
hierM1.2800.0121.183
hierMde0.3600.0080.370
image-methods1.6080.0001.608
kmeansM1.4120.0241.504
kmeansMde0.3560.0000.355
loadData000
normLoc2.1930.0042.202
normOLIN0.0600.0080.069
normRepLoess0.0640.0040.069
normScaleLimma11.864 0.40812.337
normScaleMarray2.3560.1362.494
plot-methods7.7490.0368.124
plotGenePair0.0960.0040.100
print-methods0.1320.0040.137
relNet2TGF0.1320.0000.133
relNetworkB1.6320.0001.636
relNetworkM0.0880.0040.089
robustCorr0.0000.0000.001
selSpots0.1960.0040.201
show-methods0.1360.0040.141
somM1.5320.0241.540
somMde0.3720.0040.403
summarizeReplicates1.6560.0041.665
summary-methods0.1440.0000.144
tableClass0.6840.0080.692
tablesDE3.3650.0483.418