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BioC 2.13: CHECK report for CSAR on zin1

This page was generated on 2014-04-05 09:47:49 -0700 (Sat, 05 Apr 2014).

Package 178/750HostnameOS / ArchBUILDCHECKBUILD BIN
CSAR 1.14.0
Jose M Muino
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/CSAR
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: CSAR
Version: 1.14.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings CSAR_1.14.0.tar.gz
StartedAt: 2014-04-05 00:34:26 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:36:27 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 121.0 seconds
RetCode: 0
Status:  OK 
CheckDir: CSAR.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/CSAR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CSAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CSAR’ version ‘1.14.0’
* 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 ‘CSAR’ can be installed ... [8s/8s] 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘CSAR.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [45s/45s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
CSAR-package           7.792  0.028   7.834
getThreshold           7.637  0.004   7.656
permutatedWinScores    6.924  0.008   6.947
getPermutatedWinScores 6.720  0.000   6.780
* 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-2.13-bioc/meat/CSAR.Rcheck/00check.log’
for details.

CSAR.Rcheck/00install.out:

* installing *source* package ‘CSAR’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c CSAR.c -o CSAR.o
gcc -std=gnu99 -shared -L/usr/local/lib -o CSAR.so CSAR.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/CSAR.Rcheck/CSAR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
No methods found in "GenomicRanges" for requests: unique
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "GenomicRanges" for requests: unique
* DONE (CSAR)

CSAR.Rcheck/CSAR-Ex.timings:

nameusersystemelapsed
CSAR-package7.7920.0287.834
ChIPseqScore1.8400.0041.846
distance2Genes2.4480.0002.452
genesWithPeaks2.4610.0002.464
getPermutatedWinScores6.720.006.78
getThreshold7.6370.0047.656
loadMappedReads0.0040.0000.002
mappedReads2Nhits0.8680.0000.872
permutatedWinScores6.9240.0086.947
sampleSEP3_test0.0040.0000.004
score2wig2.0160.0002.026
sigWin2.5440.0002.577