COHCAP 1.20.0
Charles Warden
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/COHCAP | | Branch: RELEASE_3_5 | | Last Commit: 34349c6 | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / 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 && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=COHCAP.buildbin-libdir COHCAP_1.20.0.tar.gz >COHCAP.Rcheck\00install.out 2>&1 && cp COHCAP.Rcheck\00install.out COHCAP-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=COHCAP.buildbin-libdir --install="check:COHCAP-install.out" --force-multiarch --no-vignettes --timings COHCAP_1.20.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/COHCAP.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.20.0'
* 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 'ref'
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'
Undefined global functions or variables:
COHCAP.27k COHCAP.450k.HMM COHCAP.450k.UCSC na.rm ref
* 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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
COHCAP.avg.by.island 4.29 0.05 7.78
COHCAP.integrate.avg.by.island 3.40 0.07 8.72
COHCAP.integrate.avg.by.site 2.92 0.12 8.05
COHCAP.avg.by.site 2.88 0.14 5.81
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
COHCAP.avg.by.island 4.55 0.14 8.42
COHCAP.integrate.avg.by.island 3.48 0.19 9.49
COHCAP.integrate.avg.by.site 2.63 0.15 6.53
COHCAP.denovo 2.53 0.11 5.26
COHCAP.avg.by.site 2.44 0.13 5.38
* 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
'C:/Users/biocbuild/bbs-3.5-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_1.20.0.zip
* DONE (COHCAP)