Bart P.P. van Houte
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/CGHnormaliter |
| Branch: RELEASE_3_9 |
| Last Commit: 27d2f41 |
| Last Changed Date: 2019-05-02 11:53:12 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:22:59 -0400 (Wed, 16 Oct 2019).
| Package 244/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CGHnormaliter 1.38.0 Bart P.P. van Houte
| 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: CGHnormaliter |
| Version: 1.38.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CGHnormaliter.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CGHnormaliter_1.38.0.tar.gz |
| StartedAt: 2019-10-16 02:34:53 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:37:46 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 172.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CGHnormaliter.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:CGHnormaliter.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CGHnormaliter_1.38.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CGHnormaliter.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 'CGHnormaliter/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CGHnormaliter' version '1.38.0'
* 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 'CGHnormaliter' 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.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'CGHbase' 'CGHcall'
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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plotMA: no visible global function definition for 'pdf'
.plotMA: no visible global function definition for 'palette'
.plotMA: no visible global function definition for 'par'
.plotMA: no visible global function definition for 'plot'
.plotMA: no visible global function definition for 'title'
.plotMA: no visible global function definition for 'abline'
.plotMA: no visible global function definition for 'dev.off'
.readCghRaw: no visible global function definition for 'read.table'
.readCghRaw: no visible global function definition for 'make_cghRaw'
.runCGHcall: no visible global function definition for 'capture.output'
.runCGHcall: no visible global function definition for 'ExpandCGHcall'
CGHnormaliter: no visible binding for global variable 'segment'
CGHnormaliter: no visible global function definition for
'capture.output'
CGHnormaliter: no visible global function definition for 'normalize'
CGHnormaliter: no visible global function definition for
'postsegnormalize'
CGHnormaliter.write.table: no visible global function definition for
'segmented'
CGHnormaliter.write.table: no visible global function definition for
'calls'
Undefined global functions or variables:
ExpandCGHcall abline calls capture.output dev.off make_cghRaw
normalize palette par pdf plot postsegnormalize read.table segment
segmented title
Consider adding
importFrom("grDevices", "dev.off", "palette", "pdf")
importFrom("graphics", "abline", "par", "plot", "title")
importFrom("utils", "capture.output", "read.table")
to your NAMESPACE file.
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
CGHnormaliter 53 0.08 53.55
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
CGHnormaliter 60.8 0.1 60.9
* 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:/Users/biocbuild/bbs-3.9-bioc/meat/CGHnormaliter.Rcheck/00check.log'
for details.
CGHnormaliter.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/CGHnormaliter_1.38.0.tar.gz && rm -rf CGHnormaliter.buildbin-libdir && mkdir CGHnormaliter.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CGHnormaliter.buildbin-libdir CGHnormaliter_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CGHnormaliter_1.38.0.zip && rm CGHnormaliter_1.38.0.tar.gz CGHnormaliter_1.38.0.zip
###
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install for i386
* installing *source* package 'CGHnormaliter' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CGHnormaliter'
finding HTML links ... done
CGHnormaliter-internal html
CGHnormaliter-package html
CGHnormaliter html
CGHnormaliter.write.table html
Leukemia 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 'CGHnormaliter' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CGHnormaliter' as CGHnormaliter_1.38.0.zip
* DONE (CGHnormaliter)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CGHnormaliter' successfully unpacked and MD5 sums checked
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CGHnormaliter.Rcheck/examples_i386/CGHnormaliter-Ex.timings
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CGHnormaliter.Rcheck/examples_x64/CGHnormaliter-Ex.timings
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