CGHcall 2.38.0
Mark van de Wiel
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/CGHcall | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | 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:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CGHcall.buildbin-libdir CGHcall_2.38.0.tar.gz >CGHcall.Rcheck\00install.out 2>&1 && cp CGHcall.Rcheck\00install.out CGHcall-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CGHcall.buildbin-libdir --install="check:CGHcall-install.out" --force-multiarch --no-vignettes --timings CGHcall_2.38.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/CGHcall.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '2.38.0'
* 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: FALSE
* 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
.callFromSeg: no visible global function definition for 'new'
.changepoints.sdundo2 : <anonymous>: no visible global function
definition for 'median'
.changepoints2: no visible global function definition for 'mad'
.changepoints2: no visible global function definition for
'changepoints.prune'
.makeEmptyFeatureData: no visible global function definition for 'is'
.makeEmptyFeatureData: no visible global function definition for 'new'
.profreg: no visible binding for global variable 'profile'
.segFromRaw: no visible global function definition for 'new'
.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'
.varregtimescount: no visible global function definition for 'var'
CGHcall: no visible global function definition for 'mad'
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 'optim'
CGHcall: no visible global function definition for 'sfRemoveAll'
CGHcall: no visible global function definition for 'sfStop'
ExpandCGHcall: no visible global function definition for 'new'
normalize: no visible global function definition for 'median'
postsegnormalize: no visible global function definition for 'median'
Undefined global functions or variables:
changepoints.prune default.DNAcopy.bdry is mad median new optim
profile sfExport sfInit sfLibrary sfRemoveAll sfSapply sfStop var
Consider adding
importFrom("methods", "is", "new")
importFrom("stats", "mad", "median", "optim", "profile", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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' ... OK
** running examples for arch 'x64' ... 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:/Users/biocbuild/bbs-3.5-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_2.38.0.zip
* DONE (CGHcall)