HTSanalyzeR 2.23.0
Xin Wang
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/HTSanalyzeR | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ WARNINGS ] | OK | |
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### Running command:
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### rm -rf HTSanalyzeR.buildbin-libdir HTSanalyzeR.Rcheck && mkdir HTSanalyzeR.buildbin-libdir HTSanalyzeR.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HTSanalyzeR.buildbin-libdir HTSanalyzeR_2.23.0.tar.gz >HTSanalyzeR.Rcheck\00install.out 2>&1 && cp HTSanalyzeR.Rcheck\00install.out HTSanalyzeR-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=HTSanalyzeR.buildbin-libdir --install="check:HTSanalyzeR-install.out" --force-multiarch --no-vignettes --timings HTSanalyzeR_2.23.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/HTSanalyzeR.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HTSanalyzeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HTSanalyzeR' version '2.23.0'
* 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 'HTSanalyzeR' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import by 'GSEABase::union' when loading 'HTSanalyzeR'
See 'c:/biocbld/bbs-3.3-bioc/meat/HTSanalyzeR.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'igraph'
A package should be listed in only one of these fields.
* 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' calls in package code:
'org.Ce.eg.db' 'org.Dm.eg.db' 'org.Hs.eg.db' 'org.Mm.eg.db'
'org.Rn.eg.db'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: '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
File 'HTSanalyzeR/R/zzz.R':
.onLoad calls:
packageStartupMessage("/////////////////////////////////////////////////////////////////////////////\n\n//------------------ Thanks for using HTSanalyzeR -------------------//\n \n//------------please use function changes() to see new changes-------------//\n\n//------------please report any bug to xinwang2hms@gmail.com---------------//\n\n/////////////////////////////////////////////////////////////////////////////\n", appendLF = FALSE)
See section 'Good practice' in '?.onAttach'.
appendGSTerms,GSCA : appendKEGGTerm: warning in mget(gsKEGG, env =
KEGGPATHID2NAME, ifnotfound = NA): partial argument match of 'env' to
'envir'
HTSanalyzeR4cellHTS2: no visible global function definition for 'fData'
KeggGeneSets: no visible binding for global variable 'KEGGPATHID2EXTID'
cellHTS2OutputStatTests: no visible global function definition for
'fData'
gseaScoresBatchParallel: no visible global function definition for
'parSapply'
appendGSTerms,GSCA : appendKEGGTerm: no visible binding for global
variable 'KEGGPATHID2NAME'
Undefined global functions or variables:
KEGGPATHID2EXTID KEGGPATHID2NAME fData parSapply
* 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' ... [20s] OK
** running examples for arch 'x64' ... [20s] 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 WARNING, 3 NOTEs
See
'c:/biocbld/bbs-3.3-bioc/meat/HTSanalyzeR.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'HTSanalyzeR' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by 'GSEABase::union' when loading 'HTSanalyzeR'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by 'GSEABase::union' when loading 'HTSanalyzeR'
install for x64
* installing *source* package 'HTSanalyzeR' ...
** testing if installed package can be loaded
Warning: replacing previous import by 'GSEABase::union' when loading 'HTSanalyzeR'
* MD5 sums
packaged installation of 'HTSanalyzeR' as HTSanalyzeR_2.23.0.zip
* DONE (HTSanalyzeR)