BioC 3.1: CHECK report for sincell on petty
This page was generated on 2015-10-09 09:37:17 -0700 (Fri, 09 Oct 2015).
sincell 1.0.0 Miguel Juliá , Antonio Rausell
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/sincell | Last Changed Rev: 102591 / Revision: 109384 | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
Summary
Package: sincell |
Version: 1.0.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sincell_1.0.0.tar.gz |
StartedAt: 2015-10-09 02:04:40 -0700 (Fri, 09 Oct 2015) |
EndedAt: 2015-10-09 02:06:30 -0700 (Fri, 09 Oct 2015) |
EllapsedTime: 110.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sincell.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sincell_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/sincell.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.0.0’
* 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 ... [30s/30s] 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 ... [31s/11s] OK
Examples with CPU or elapsed time > 5s
user system
sc_StatisticalSupportByGeneSubsampling 16.506 1.036
sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates 7.675 0.850
elapsed
sc_StatisticalSupportByGeneSubsampling 6.080
sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates 0.993
* 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-3.1-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-3.1-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:
name | user | system | elapsed
|
f_distance2vector | 0.002 | 0.000 | 0.003 |
|
sc_AssociationOfCellsHierarchyWithAGeneSet | 0.067 | 0.004 | 0.072 |
|
sc_ComparissonOfGraphs | 0.094 | 0.004 | 0.098 |
|
sc_DimensionalityReductionObj | 0.392 | 0.006 | 0.398 |
|
sc_GraphBuilderObj | 0.106 | 0.003 | 0.110 |
|
sc_InSilicoCellsReplicatesObj | 0.059 | 0.043 | 0.104 |
|
sc_InitializingSincellObject | 0.039 | 0.008 | 0.047 |
|
sc_StatisticalSupportByGeneSubsampling | 16.506 | 1.036 | 6.080 |
|
sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates | 7.675 | 0.850 | 0.993 |
|
sc_clusterObj | 0.074 | 0.011 | 0.086 |
|
sc_distanceObj | 0.191 | 0.032 | 0.223 |
|
sc_marker2color | 0.020 | 0.001 | 0.020 |
|