STRINGdb 1.5.5
Andrea Franceschini , Alexander Roth , Christian Von Mering , Michael Kuhn , Lars J Jensen
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/STRINGdb | | Last Changed Rev: 98967 / Revision: 102249 | | Last Changed Date: 2015-02-02 10:07:39 -0800 (Mon, 02 Feb 2015) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | ERROR | OK |
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### Running command:
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### rm -rf STRINGdb.buildbin-libdir STRINGdb.Rcheck && mkdir STRINGdb.buildbin-libdir STRINGdb.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=STRINGdb.buildbin-libdir STRINGdb_1.5.5.tar.gz >STRINGdb.Rcheck\00install.out 2>&1 && cp STRINGdb.Rcheck\00install.out STRINGdb-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=STRINGdb.buildbin-libdir --install="check:STRINGdb-install.out" --force-multiarch --no-vignettes --timings STRINGdb_1.5.5.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/STRINGdb.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'STRINGdb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'STRINGdb' version '1.5.5'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'png' 'sqldf' 'plyr' 'igraph' 'RCurl' 'plotrix' 'RColorBrewer'
'gplots' 'hash'
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 'STRINGdb' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
doc 5.1Mb
* 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
* 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:
'RColorBrewer' 'RCurl' 'gplots' 'hash' 'igraph' 'methods' 'plotrix'
'plyr' 'png' 'sqldf'
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
get_STRING_species: no visible binding for global variable
'official_name'
postFormSmart: no visible global function definition for 'curlOptions'
postFormSmart: no visible global function definition for
'getCurlHandle'
postFormSmart: no visible binding for global variable 'curlEscape'
postFormSmart: no visible global function definition for 'postForm'
ppi_enrichment: no visible global function definition for 'V'
ppi_enrichment: no visible global function definition for 'ecount'
ppi_enrichment: no visible global function definition for
'induced.subgraph'
ppi_enrichment: no visible global function definition for 'degree'
ppi_enrichment_full: no visible global function definition for 'V'
ppi_enrichment_full: no visible global function definition for 'ecount'
ppi_enrichment_full: no visible global function definition for
'induced.subgraph'
ppi_enrichment_full: no visible global function definition for 'degree'
ppie.getNumEdgesBetween: no visible global function definition for
'neighborhood'
* 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' ... [11m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
STRINGdb-package 257.24 2.57 382.59
STRINGdb 197.05 1.70 257.61
** running examples for arch 'x64' ... [11m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
STRINGdb-package 288.57 3.89 405.40
STRINGdb 217.31 2.73 258.26
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [248s]
[248s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [254s]
[254s] 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
NOTE: There were 4 notes.
See
'D:/biocbld/bbs-3.0-bioc/meat/STRINGdb.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'STRINGdb' ...
** 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 'STRINGdb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'STRINGdb' as STRINGdb_1.5.5.zip
* DONE (STRINGdb)