SomatiCA 1.15.0
Mengjie Chen
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SomatiCA | | 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 | NotNeeded | OK | WARNINGS | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
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### Running command:
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### rm -rf SomatiCA.buildbin-libdir SomatiCA.Rcheck && mkdir SomatiCA.buildbin-libdir SomatiCA.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SomatiCA.buildbin-libdir SomatiCA_1.15.0.tar.gz >SomatiCA.Rcheck\00install.out 2>&1 && cp SomatiCA.Rcheck\00install.out SomatiCA-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=SomatiCA.buildbin-libdir --install="check:SomatiCA-install.out" --force-multiarch --no-vignettes --timings SomatiCA_1.15.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/SomatiCA.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 'SomatiCA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SomatiCA' version '1.15.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'SomatiCAData'
Depends: includes the non-default packages:
'lars' 'DNAcopy' 'foreach' 'rebmix' 'GenomicRanges' 'IRanges'
'doParallel'
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 'SomatiCA' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import by 'IRanges::sd' when loading 'SomatiCA'
See 'c:/biocbld/bbs-3.3-bioc/meat/SomatiCA.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'foreach' 'lars' 'DNAcopy' 'methods' 'rebmix' 'GenomicRanges' 'IRanges' 'sn'
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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
'DNAcopy' 'doParallel' 'foreach' 'lars' 'rebmix'
Please remove these calls from your code.
'library' or 'require' call to 'sn' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'methods'
All declared Imports should be used.
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
refineSegment: no visible global function definition for 'sn.mle'
somaticRatio: no visible global function definition for 'sn.mle'
Undefined global functions or variables:
sn.mle
* 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' ... [38s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
SomatiCApipe 15.19 0.01 15.21
admixtureRate 14.36 0.02 14.37
** running examples for arch 'x64' ... [42s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
admixtureRate 17.13 0.02 17.14
SomatiCApipe 16.30 0.08 16.37
* 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, 4 NOTEs
See
'c:/biocbld/bbs-3.3-bioc/meat/SomatiCA.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'SomatiCA' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by 'IRanges::sd' when loading 'SomatiCA'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by 'IRanges::sd' when loading 'SomatiCA'
install for x64
* installing *source* package 'SomatiCA' ...
** testing if installed package can be loaded
Warning: replacing previous import by 'IRanges::sd' when loading 'SomatiCA'
* MD5 sums
packaged installation of 'SomatiCA' as SomatiCA_1.15.0.zip
* DONE (SomatiCA)