CGHcall 2.33.0
Mark van de Wiel
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CGHcall | | 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 | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | |
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### Running command:
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### rm -rf CGHcall.buildbin-libdir CGHcall.Rcheck && mkdir CGHcall.buildbin-libdir CGHcall.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CGHcall.buildbin-libdir CGHcall_2.33.0.tar.gz >CGHcall.Rcheck\00install.out 2>&1 && cp CGHcall.Rcheck\00install.out CGHcall-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=CGHcall.buildbin-libdir --install="check:CGHcall-install.out" --force-multiarch --no-vignettes --timings CGHcall_2.33.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/CGHcall.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 'CGHcall/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CGHcall' version '2.33.0'
* 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 'CGHcall' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Non-standard license specification:
GPL (http://www.gnu.org/copyleft/gpl.html)
Standardizable: TRUE
Standardized license specification:
GPL
* 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' call to 'snowfall' which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
'DNAcopy' 'methods' 'snowfall'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
':::' call which should be '::': 'DNAcopy:::getbdry'
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
'Biobase:::assayDataDims' 'DNAcopy:::trimmed.variance'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'.MakeData' '.alpha0all' '.assignNames' '.callFromSeg' '.countcl'
'.posteriorp' '.reallik4' '.segFromRaw' '.sumreg' '.sumsqreg'
'.totallik' '.varproffun' '.varregtimescount'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
.Fortran("fndcpt", ..., PACKAGE = "DNAcopy")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
.changepoints2: no visible global function definition for
'changepoints.prune'
.segment2: no visible binding for global variable
'default.DNAcopy.bdry'
.totallik: no visible global function definition for 'sfExport'
.totallik: no visible global function definition for 'sfSapply'
CGHcall: no visible global function definition for 'sfInit'
CGHcall: no visible global function definition for 'sfLibrary'
CGHcall: no visible global function definition for 'sfExport'
CGHcall: no visible global function definition for 'sfRemoveAll'
CGHcall: no visible global function definition for 'sfStop'
Undefined global functions or variables:
changepoints.prune default.DNAcopy.bdry sfExport sfInit sfLibrary
sfRemoveAll sfSapply sfStop
* 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' ... [2s] OK
** running examples for arch 'x64' ... [2s] 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: 4 NOTEs
See
'c:/biocbld/bbs-3.3-bioc/meat/CGHcall.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'CGHcall' ...
** 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 'CGHcall' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CGHcall' as CGHcall_2.33.0.zip
* DONE (CGHcall)