altcdfenvs 2.34.0
Laurent Gautier
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/altcdfenvs | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf altcdfenvs.buildbin-libdir altcdfenvs.Rcheck && mkdir altcdfenvs.buildbin-libdir altcdfenvs.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=altcdfenvs.buildbin-libdir altcdfenvs_2.34.0.tar.gz >altcdfenvs.Rcheck\00install.out 2>&1 && cp altcdfenvs.Rcheck\00install.out altcdfenvs-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=altcdfenvs.buildbin-libdir --install="check:altcdfenvs-install.out" --force-multiarch --no-vignettes --timings altcdfenvs_2.34.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/altcdfenvs.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'altcdfenvs/DESCRIPTION' ... OK
* this is package 'altcdfenvs' version '2.34.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics' 'S4Vectors' 'Biobase' 'affy' 'makecdfenv' 'Biostrings'
'hypergraph'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'altcdfenvs' 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
Packages in Depends field not imported from:
'Biobase' 'Biostrings' 'hypergraph' 'makecdfenv' 'methods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
buildCdfEnv.biostrings: no visible global function definition for
'update'
buildCdfEnv.biostrings: no visible global function definition for
'xy2indices'
buildCdfEnv.matchprobes: no visible global function definition for
'update'
buildCdfEnv.matchprobes: no visible global function definition for
'xy2indices'
copyCdfEnvAffy: no visible global function definition for 'copyEnv'
getCdfEnvAffy: no visible global function definition for 'getCdfInfo'
index2xy.CdfEnvAffy: no visible global function definition for
'indices2xy'
matchAffyProbes: no visible global function definition for
'DNAStringSet'
matchAffyProbes: no visible global function definition for 'DNAString'
matchAffyProbes: no visible global function definition for 'PDict'
matchAffyProbes: no visible global function definition for 'matchPDict'
xy2index.CdfEnvAffy: no visible global function definition for
'xy2indices'
toHypergraph,AffyProbesMatch : <anonymous>: no visible global function
definition for 'Hyperedge'
toHypergraph,CdfEnvAffy : <anonymous>: no visible global function
definition for 'Hyperedge'
Undefined global functions or variables:
DNAString DNAStringSet Hyperedge PDict copyEnv getCdfInfo indices2xy
matchPDict update xy2indices
Consider adding
importFrom("stats", "update")
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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
removeIndex 10.41 0.00 10.95
matchAffyProbes 5.48 0.10 9.43
CdfEnvAffy-class 5.03 0.02 7.75
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
removeIndex 14.63 0.04 14.66
matchAffyProbes 6.41 0.12 6.53
CdfEnvAffy-class 5.26 0.05 5.31
* 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: 4 NOTEs
See
'E:/biocbld/bbs-3.3-bioc/meat/altcdfenvs.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'altcdfenvs' ...
** R
** data
** inst
** preparing package for lazy loading
NOTE: arguments in definition for validity method for class 'AffyProbesMatch' changed from (obj) to (object)
in method for 'toHypergraph' with signature '"CdfEnvAffy"': no definition for class "CdfEnvAffy"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'altcdfenvs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'altcdfenvs' as altcdfenvs_2.34.0.zip
* DONE (altcdfenvs)