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BioC 3.2: CHECK report for sincell on perceval

This page was generated on 2015-11-06 13:11:22 -0800 (Fri, 06 Nov 2015).

Package 981/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sincell 1.2.0
Miguel Julia , Antonio Rausell
Snapshot Date: 2015-11-05 16:24:12 -0800 (Thu, 05 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/sincell
Last Changed Rev: 109589 / Revision: 110379
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sincell
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sincell_1.2.0.tar.gz
StartedAt: 2015-11-06 10:09:59 -0800 (Fri, 06 Nov 2015)
EndedAt: 2015-11-06 10:11:15 -0800 (Fri, 06 Nov 2015)
EllapsedTime: 76.5 seconds
RetCode: 0
Status:  OK 
CheckDir: sincell.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sincell_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/sincell.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sincell/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sincell’ version ‘1.2.0’
* package encoding: UTF-8
* 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 ‘sincell’ can be installed ... [21s/21s] 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 compiled code ... NOTE
File ‘sincell/libs/sincell.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘pseudoreplicatesbymodel.o’, ‘pseudoreplicatesbynoise.o’,
      ‘pseudoreplicatesbynoise_cv2.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘pseudoreplicatesbymodel.o’, ‘pseudoreplicatesbynoise.o’,
      ‘pseudoreplicatesbynoise_cv2.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [22s/8s] OK
Examples with CPU or elapsed time > 5s
                                                                user system
sc_StatisticalSupportByGeneSubsampling                        11.442  0.827
sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates  4.904  0.566
                                                              elapsed
sc_StatisticalSupportByGeneSubsampling                          4.360
sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates   0.693
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/sincell.Rcheck/00check.log’
for details.


sincell.Rcheck/00install.out:

* installing *source* package ‘sincell’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c RcppExports.cpp -o RcppExports.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c pseudoreplicatesbymodel.cpp -o pseudoreplicatesbymodel.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c pseudoreplicatesbynoise.cpp -o pseudoreplicatesbynoise.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c pseudoreplicatesbynoise_cv2.cpp -o pseudoreplicatesbynoise_cv2.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c sstalgorithm.cpp -o sstalgorithm.o
llvm-g++-4.2 -arch x86_64 -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 -L/usr/local/lib -o sincell.so RcppExports.o pseudoreplicatesbymodel.o pseudoreplicatesbynoise.o pseudoreplicatesbynoise_cv2.o sstalgorithm.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/sincell.Rcheck/sincell/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 (sincell)

sincell.Rcheck/sincell-Ex.timings:

nameusersystemelapsed
f_distance2vector0.0010.0010.002
sc_AssociationOfCellsHierarchyWithAGeneSet0.0450.0030.047
sc_ComparissonOfGraphs0.0620.0030.086
sc_DimensionalityReductionObj0.2660.0040.269
sc_GraphBuilderObj0.0670.0010.069
sc_InSilicoCellsReplicatesObj0.0410.0350.062
sc_InitializingSincellObject0.0280.0070.035
sc_StatisticalSupportByGeneSubsampling11.442 0.827 4.360
sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates4.9040.5660.693
sc_clusterObj0.0460.0070.053
sc_distanceObj0.1340.0220.156
sc_marker2color0.0120.0000.013