GOTHiC 1.6.0
Borbala Mifsud
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/GOTHiC | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf GOTHiC.buildbin-libdir GOTHiC.Rcheck && mkdir GOTHiC.buildbin-libdir GOTHiC.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOTHiC.buildbin-libdir GOTHiC_1.6.0.tar.gz >GOTHiC.Rcheck\00install.out 2>&1 && cp GOTHiC.Rcheck\00install.out GOTHiC-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GOTHiC.buildbin-libdir --install="check:GOTHiC-install.out" --force-multiarch --no-vignettes --timings GOTHiC_1.6.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/GOTHiC.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GOTHiC/DESCRIPTION' ... OK
* this is package 'GOTHiC' version '1.6.0'
* 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 'GOTHiC' can be installed ... OK
* checking installed package size ... OK
* 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
Unexported object imported by a ':::' call: 'S4Vectors:::orderIntegerPairs'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.binInteractions: no visible binding for global variable 'chr1'
.binInteractions: no visible binding for global variable 'chr2'
.binInteractions: no visible binding for global variable 'locus1'
.binInteractions: no visible binding for global variable 'locus2'
.binomialHiC: no visible binding for global variable 'resGR'
.binomialHiC : <anonymous>: no visible binding for global variable
'frequencies'
.binomialHiC : <anonymous>: no visible binding for global variable
'int1'
.binomialHiC : <anonymous>: no visible binding for global variable
'int2'
.binomialHiC: no visible binding for global variable 'V1'
.binomialHiC: no visible binding for global variable 'int1'
.binomialHiC: no visible binding for global variable 'int2'
.binomialHiC: no visible binding for global variable 'frequencies'
.binomialHiC: no visible binding for global variable 'pvalue'
.binomialHiChicup : <anonymous>: no visible binding for global variable
'frequencies'
.binomialHiChicup : <anonymous>: no visible binding for global variable
'int1'
.binomialHiChicup : <anonymous>: no visible binding for global variable
'int2'
.binomialHiChicup: no visible binding for global variable 'V1'
.binomialHiChicup: no visible binding for global variable 'int1'
.binomialHiChicup: no visible binding for global variable 'int2'
.binomialHiChicup: no visible binding for global variable 'frequencies'
.binomialHiChicup: no visible binding for global variable 'pvalue'
.findOverlaps.parallel : <anonymous>: no visible global function
definition for 'isCircular'
.findOverlaps.parallel : <anonymous>: no visible global function
definition for 'seqlengths'
.getRestrictionSitesFromBSgenome: no visible global function definition
for 'biocLite'
.getRestrictionSitesFromBSgenome: no visible global function definition
for 'seqlengths'
GOTHiC: no visible binding for global variable
'BSgenome.Hsapiens.UCSC.hg19'
GOTHiC: no visible binding for global variable 'filtered'
GOTHiC: no visible binding for global variable 'interactingLoci'
mapReadsToRestrictionSites: no visible binding for global variable
'resGR'
* 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' ... [63s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
GOTHiC 40.44 1.74 44.17
GOTHiChicup 6.42 0.28 6.70
** running examples for arch 'x64' ... [57s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
GOTHiC 36.40 1.79 38.20
GOTHiChicup 6.58 0.20 6.78
* 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: 2 NOTEs
See
'C:/biocbld/bbs-3.2-bioc/meat/GOTHiC.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'GOTHiC' ...
** 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 'GOTHiC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOTHiC' as GOTHiC_1.6.0.zip
* DONE (GOTHiC)