Laurent Gautier
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/altcdfenvs |
| Branch: RELEASE_3_9 |
| Last Commit: 90a11e7 |
| Last Changed Date: 2019-05-02 11:53:02 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:19:16 -0400 (Wed, 16 Oct 2019).
| Package 46/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| altcdfenvs 2.46.0 Laurent Gautier
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: altcdfenvs |
| Version: 2.46.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:altcdfenvs.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings altcdfenvs_2.46.0.tar.gz |
| StartedAt: 2019-10-16 01:53:34 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:56:09 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 155.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: altcdfenvs.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:altcdfenvs.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings altcdfenvs_2.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/altcdfenvs.Rcheck' * using R version 3.6.1 (2019-07-05) * 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 '2.46.0' * 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 ... NOTE Found the following apparent S3 methods exported but not registered: plot.CdfEnvAffy print.FASTA unique.CdfEnvAffy See section 'Registering S3 methods' in the 'Writing R Extensions' manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE buildCdfEnv.biostrings: no visible global function definition for 'validObject' buildCdfEnv.biostrings: no visible global function definition for 'is' buildCdfEnv.biostrings: no visible global function definition for 'new' 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 'is' buildCdfEnv.matchprobes: no visible global function definition for 'new' 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' countduplicated: no visible global function definition for 'is' countduplicated: no visible global function definition for 'as' geneNames.CdfEnvAffy: no visible global function definition for 'as' getCdfEnvAffy: no visible global function definition for 'is' getCdfEnvAffy: no visible global function definition for 'getCdfInfo' index2xy.CdfEnvAffy: no visible global function definition for 'indices2xy' indexProbes.CdfEnvAffy: no visible global function definition for 'as' 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' matchAffyProbes: no visible global function definition for 'new' removeIndex: no visible global function definition for 'as' unique.CdfEnvAffy: no visible global function definition for 'as' validAffyBatch: no visible global function definition for 'is' validCdfEnvAffy: no visible global function definition for 'as' wrapCdfEnvAffy: no visible global function definition for 'new' xy2index.CdfEnvAffy: no visible global function definition for 'xy2indices' [,CdfEnvAffy-character-missing-missing: no visible global function definition for 'as' coerce,CdfEnvAffy-Cdf: no visible global function definition for 'new' combine,AffyProbesMatch-AffyProbesMatch: no visible global function definition for 'new' geneNames,CdfEnvAffy: no visible global function definition for 'as' indexProbes,CdfEnvAffy-character: no visible global function definition for 'as' show,CdfEnvAffy: no visible global function definition for 'as' toHypergraph,AffyProbesMatch :: no visible global function definition for 'Hyperedge' toHypergraph,AffyProbesMatch: no visible global function definition for 'new' toHypergraph,CdfEnvAffy : : no visible global function definition for 'Hyperedge' toHypergraph,CdfEnvAffy: no visible global function definition for 'new' Undefined global functions or variables: DNAString DNAStringSet Hyperedge PDict as copyEnv getCdfInfo indices2xy is matchPDict new update validObject xy2indices Consider adding importFrom("methods", "as", "is", "new", "validObject") importFrom("stats", "update") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed removeIndex 7.59 0.13 7.91 matchAffyProbes 4.69 0.31 5.42 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed matchAffyProbes 6.58 0.30 6.88 removeIndex 6.83 0.04 6.87 * 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: 5 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/altcdfenvs.Rcheck/00check.log' for details.
altcdfenvs.Rcheck/00install.out
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/altcdfenvs_2.46.0.tar.gz && rm -rf altcdfenvs.buildbin-libdir && mkdir altcdfenvs.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=altcdfenvs.buildbin-libdir altcdfenvs_2.46.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL altcdfenvs_2.46.0.zip && rm altcdfenvs_2.46.0.tar.gz altcdfenvs_2.46.0.zip
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install for i386
* installing *source* package 'altcdfenvs' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare 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
converting help for package 'altcdfenvs'
finding HTML links ... done
AffyProbesMatch-class html
CdfEnvAffy-class html
appendCdfEnvAffy html
buildCdfEnv.biostrings html
cdfenv html
cdfenvEx html
copyCdfEnvAffy html
countduplicated html
geneNames html
getxy.probeseq html
index2xy html
indexProbes.CdfEnvAffy html
matchAffyProbes html
plot.CdfEnvAffy html
removeIndex html
toHypergraph html
unique.CdfEnvAffy html
utils.FASTA html
validAffyBatch html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'altcdfenvs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'altcdfenvs' as altcdfenvs_2.46.0.zip
* DONE (altcdfenvs)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'altcdfenvs' successfully unpacked and MD5 sums checked
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altcdfenvs.Rcheck/examples_i386/altcdfenvs-Ex.timings
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altcdfenvs.Rcheck/examples_x64/altcdfenvs-Ex.timings
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