SGSeq 1.8.1
Leonard Goldstein
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/SGSeq | | Last Changed Rev: 124760 / Revision: 128728 | | Last Changed Date: 2016-12-02 21:05:54 -0500 (Fri, 02 Dec 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | 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 && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SGSeq.buildbin-libdir SGSeq_1.8.1.tar.gz >SGSeq.Rcheck\00install.out 2>&1 && cp SGSeq.Rcheck\00install.out SGSeq-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=SGSeq.buildbin-libdir --install="check:SGSeq-install.out" --force-multiarch --no-vignettes --timings SGSeq_1.8.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/SGSeq.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.8.1'
* 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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
predictVariantEffects 21.97 0.05 22.01
analyzeFeatures 15.00 0.19 15.19
predictTxFeatures 8.22 0.09 8.32
getSGVariantCounts 6.20 0.05 6.25
getSGFeatureCounts 5.55 0.12 5.67
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
predictVariantEffects 35.64 0.05 35.68
analyzeFeatures 23.66 0.47 24.13
predictTxFeatures 11.64 0.20 11.85
getSGVariantCounts 7.52 0.14 7.66
getSGFeatureCounts 5.97 0.14 6.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
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
'C:/Users/biocbuild/bbs-3.4-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_1.8.1.zip
* DONE (SGSeq)