goseq 1.25.0
Nadia Davidson , Anthony Hawkins
| Snapshot Date: 2016-05-04 16:20:12 -0700 (Wed, 04 May 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/goseq | | Last Changed Rev: 117081 / Revision: 117135 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | [ OK ] | OK |  |
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### Running command:
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### rm -rf goseq.buildbin-libdir goseq.Rcheck && mkdir goseq.buildbin-libdir goseq.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=goseq.buildbin-libdir goseq_1.25.0.tar.gz >goseq.Rcheck\00install.out 2>&1 && cp goseq.Rcheck\00install.out goseq-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=goseq.buildbin-libdir --install="check:goseq-install.out" --force-multiarch --no-vignettes --timings goseq_1.25.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/goseq.Rcheck'
* using R version 3.3.0 RC (2016-04-28 r70561)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'goseq/DESCRIPTION' ... OK
* this is package 'goseq' version '1.25.0'
* 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 'goseq' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
* 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 dependencies in R code ... NOTE
'library' or 'require' call to 'rtracklayer' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.onAttach: no visible global function definition for 'winMenuAddItem'
getgo: no visible global function definition for 'toTable'
getlength: no visible global function definition for
'installed.packages'
getlength: no visible global function definition for 'tail'
getlength: no visible global function definition for 'toTable'
getlength: no visible global function definition for
'transcriptLengths'
getlength: no visible global function definition for 'browserSession'
getlength: no visible global function definition for 'genome<-'
getlength: no visible global function definition for 'ucscTableQuery'
getlength: no visible global function definition for 'getTable'
supportedOrganisms: no visible global function definition for
'ucscGenomes'
Undefined global functions or variables:
browserSession genome<- getTable installed.packages tail toTable
transcriptLengths ucscGenomes ucscTableQuery winMenuAddItem
Consider adding
importFrom("utils", "installed.packages", "tail", "winMenuAddItem")
to your NAMESPACE file.
* 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' ... [90s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
goseq 38.69 1.00 40.00
getgo 17.77 0.76 18.53
nullp 7.32 0.38 7.69
plotPWF 6.64 0.40 7.05
getlength 4.37 0.50 6.56
** running examples for arch 'x64' ... [115s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
goseq 44.59 1.35 58.91
getgo 20.14 1.11 21.26
nullp 8.16 0.25 8.46
plotPWF 7.46 0.45 8.00
getlength 4.80 0.49 5.30
* 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: 3 NOTEs
See
'D:/biocbld/bbs-3.4-bioc/meat/goseq.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'goseq' ...
** R
** data
** 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 'goseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'goseq' as goseq_1.25.0.zip
* DONE (goseq)