SGSeq 1.4.3
Leonard Goldstein
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/SGSeq | | Last Changed Rev: 113779 / Revision: 116712 | | Last Changed Date: 2016-02-18 14:43:24 -0800 (Thu, 18 Feb 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | 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 SGSeq.buildbin-libdir SGSeq.Rcheck && mkdir SGSeq.buildbin-libdir SGSeq.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SGSeq.buildbin-libdir SGSeq_1.4.3.tar.gz >SGSeq.Rcheck\00install.out 2>&1 && cp SGSeq.Rcheck\00install.out SGSeq-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=SGSeq.buildbin-libdir --install="check:SGSeq-install.out" --force-multiarch --no-vignettes --timings SGSeq_1.4.3.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/SGSeq.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SGSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SGSeq' version '1.4.3'
* 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 'SGSeq' 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 ... NOTE
Unexported objects imported by ':::' calls:
'GenomicRanges:::extraColumnSlotNames'
'GenomicRanges:::extraColumnSlotsAsDF'
See the note in ?`:::` about the use of this operator.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [80s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
predictVariantEffects 19.50 0.03 19.54
analyzeFeatures 17.21 0.14 17.42
predictTxFeatures 10.16 0.02 10.17
getSGVariantCounts 7.31 0.08 7.39
getSGFeatureCounts 6.99 0.08 7.06
** running examples for arch 'x64' ... [107s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
analyzeFeatures 22.93 0.22 23.15
predictVariantEffects 22.26 0.01 22.28
predictTxFeatures 14.37 0.11 14.48
getSGVariantCounts 11.58 0.14 11.71
getSGFeatureCounts 10.40 0.11 10.52
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [124s]
[124s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [167s]
[168s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'D:/biocbld/bbs-3.2-bioc/meat/SGSeq.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'SGSeq' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'SGSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SGSeq' as SGSeq_1.4.3.zip
* DONE (SGSeq)