Repitools 1.6.0
Mark Robinson
| Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/Repitools | | Last Changed Rev: 75263 / Revision: 81334 | | Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/Repitools.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Repitools/DESCRIPTION’ ... OK
* this is package ‘Repitools’ version ‘1.6.0’
* 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 ‘Repitools’ can be installed ... [29s/29s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files are already in R: ‘Sweave.sty’
Please remove them from your package.
* checking examples ... [4m/10m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
methylEst 47.667 1.832 261.549
BayMethList-class 33.530 0.416 37.511
empBayes 26.174 1.236 158.424
maskOut 21.865 0.552 23.576
sequenceCalc 20.590 1.308 22.411
determineOffset 21.693 0.112 22.153
cpgDensityCalc 19.313 1.356 23.103
cpgDensityPlot 13.049 0.212 13.290
findClusters 6.592 0.016 6.630
enrichmentPlot 5.673 0.012 5.736
gcContentCalc 4.697 0.628 5.573
binPlots 4.192 0.200 6.412
clusterPlots 3.624 0.208 6.149
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘tests.R’ [174s/176s]
[174s/177s] OK
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There was 1 note.
See
‘/home/biocbuild/bbs-2.12-bioc/meat/Repitools.Rcheck/00check.log’
for details.
* installing *source* package ‘Repitools’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -D R_NO_REMAP -I. -fpic -g -O2 -Wall -c const.c -o const.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -D R_NO_REMAP -I. -fpic -g -O2 -Wall -c hyp2f1.c -o hyp2f1.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -D R_NO_REMAP -I. -fpic -g -O2 -Wall -c mtherr.c -o mtherr.o
gcc -std=gnu99 -shared -L/usr/local/lib -o Repitools.so const.o hyp2f1.o mtherr.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/Repitools.Rcheck/Repitools/libs
** R
** data
** inst
** preparing package for lazy loading
in method for ‘.featureScores’ with signature ‘"AffymetrixCelSet","GRanges"’: no definition for class “AffymetrixCelSet”
in method for ‘regionStats’ with signature ‘"AffymetrixCelSet"’: no definition for class “AffymetrixCelSet”
in method for ‘writeWig’ with signature ‘"AffymetrixCelSet"’: no definition for class “AffymetrixCelSet”
in method for ‘cpgBoxplots’ with signature ‘"AffymetrixCelSet"’: no definition for class “AffymetrixCelSet”
in method for ‘.blocksStats’ with signature ‘"AffymetrixCelSet","GRanges"’: no definition for class “AffymetrixCelSet”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Repitools)