Mark van de Wiel
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/CGHcall |
| Branch: RELEASE_3_9 |
| Last Commit: 41d86f0 |
| Last Changed Date: 2019-05-02 11:53:08 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:21:25 -0400 (Wed, 16 Oct 2019).
| Package 242/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CGHcall 2.46.0 Mark van de Wiel
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: CGHcall |
| Version: 2.46.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CGHcall.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CGHcall_2.46.0.tar.gz |
| StartedAt: 2019-10-16 02:33:42 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:34:58 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 76.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CGHcall.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CGHcall.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CGHcall_2.46.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CGHcall.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '2.46.0'
* 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 : : 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 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-3.9-bioc/meat/CGHcall.Rcheck/00check.log'
for details.
CGHcall.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CGHcall_2.46.0.tar.gz && rm -rf CGHcall.buildbin-libdir && mkdir CGHcall.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CGHcall.buildbin-libdir CGHcall_2.46.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CGHcall_2.46.0.zip && rm CGHcall_2.46.0.tar.gz CGHcall_2.46.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 176k 100 176k 0 0 1376k 0 --:--:-- --:--:-- --:--:-- 1449k
install for i386
* installing *source* package 'CGHcall' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CGHcall'
finding HTML links ... done
CGHcall-package html
CGHcall html
finding level-2 HTML links ... done
ExpandCGHcall html
Wilting html
normalize html
postsegnormalize html
preprocess html
segmentData html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'CGHcall' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CGHcall' as CGHcall_2.46.0.zip
* DONE (CGHcall)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CGHcall' successfully unpacked and MD5 sums checked
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CGHcall.Rcheck/examples_i386/CGHcall-Ex.timings
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CGHcall.Rcheck/examples_x64/CGHcall-Ex.timings
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