COHCAP 1.7.0
Charles Warden
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/COHCAP | | Last Changed Rev: 102594 / Revision: 107602 | | Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf COHCAP.buildbin-libdir COHCAP.Rcheck && mkdir COHCAP.buildbin-libdir COHCAP.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=COHCAP.buildbin-libdir COHCAP_1.7.0.tar.gz >COHCAP.Rcheck\00install.out 2>&1 && cp COHCAP.Rcheck\00install.out COHCAP-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=COHCAP.buildbin-libdir --install="check:COHCAP-install.out" --force-multiarch --no-vignettes --timings COHCAP_1.7.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/COHCAP.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'COHCAP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'COHCAP' version '1.7.0'
* 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 whether package 'COHCAP' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
COHCAP.annotate: no visible binding for global variable
'COHCAP.450k.UCSC'
COHCAP.annotate: no visible binding for global variable
'COHCAP.450k.HMM'
COHCAP.annotate: no visible binding for global variable 'COHCAP.27k'
COHCAP.avg.by.site: no visible binding for global variable
'integrate.folder'
COHCAP.integrate.avg.by.island: no visible binding for global variable
'na.rm'
cor.test.est: no visible binding for global variable 'na.rm'
cor.test.pvalue: no visible binding for global variable 'na.rm'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [62s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
COHCAP.avg.by.island 3.20 0.11 10.75
COHCAP.annotate 2.82 0.03 10.50
COHCAP.integrate.avg.by.island 2.71 0.08 10.27
COHCAP.integrate.avg.by.site 2.51 0.14 12.23
COHCAP.avg.by.site 2.33 0.06 7.94
COHCAP.site 2.32 0.06 6.64
** running examples for arch 'x64' ... [76s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
COHCAP.avg.by.island 3.37 0.08 13.02
COHCAP.avg.by.site 2.33 0.04 11.27
COHCAP.integrate.avg.by.island 2.31 0.03 19.39
COHCAP.integrate.avg.by.site 2.10 0.08 13.08
COHCAP.site 2.07 0.03 12.36
* 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
'D:/biocbld/bbs-3.2-bioc/meat/COHCAP.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'COHCAP' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'COHCAP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'COHCAP' as COHCAP_1.7.0.zip
* DONE (COHCAP)