J. Zhang
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/cghMCR |
| git_branch: RELEASE_3_14 |
| git_last_commit: 669771b |
| git_last_commit_date: 2021-10-26 11:49:38 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:19 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the cghMCR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cghMCR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 288/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cghMCR 1.52.0 (landing page) J. Zhang
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: cghMCR |
| Version: 1.52.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cghMCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cghMCR_1.52.0.tar.gz |
| StartedAt: 2022-04-12 17:09:12 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 17:12:25 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 193.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: cghMCR.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cghMCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cghMCR_1.52.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/cghMCR.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cghMCR/DESCRIPTION' ... OK
* this is package 'cghMCR' version '1.52.0'
* 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 'cghMCR' can be installed ... OK
* checking installed package size ... NOTE
installed size is 98.3Mb
sub-directories of 1Mb or more:
sampleData 97.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 'DNAcopy' which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
'CNTools' 'DNAcopy' 'limma' 'methods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'adjustSegments' 'alignGenes' 'drawSegs' 'getAdjustments'
'highlightChrom' 'markChrom'
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
plot.DNAcopy
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SGOL: no visible global function definition for 'segBy'
SGOL: no visible global function definition for 'rs'
drawSegs : drawSegLine: no visible global function definition for
'lines'
dropGenes: no visible global function definition for 'approx'
getAlteredSegs: no visible global function definition for 'quantile'
getLineData: no visible global function definition for 'median'
getSegData: no visible global function definition for 'read.maimages'
getSegData: no visible global function definition for
'normalizeWithinArrays'
getSegData: no visible global function definition for
'backgroundCorrect'
getSegData: no visible global function definition for 'CNA'
getSegData: no visible global function definition for 'segment'
getSegData: no visible global function definition for 'smooth.CNA'
highlightChrom: no visible global function definition for 'polygon'
markChrom: no visible global function definition for 'polygon'
plot.DNAcopy: no visible global function definition for 'png'
plot.DNAcopy: no visible global function definition for 'par'
plot.DNAcopy: no visible global function definition for 'axis'
plot.DNAcopy: no visible global function definition for 'box'
plot.DNAcopy: no visible global function definition for 'points'
plot.DNAcopy: no visible global function definition for 'lines'
plot.DNAcopy: no visible global function definition for 'dev.off'
plot.MCR: no visible global function definition for 'png'
plot.MCR: no visible global function definition for 'par'
plot.MCR: no visible global function definition for 'dev.off'
plotSGOL: no visible global function definition for 'lines'
plotSGOL: no visible global function definition for 'axis'
plotSGOL: no visible global function definition for 'box'
showMCR : <anonymous>: no visible global function definition for
'median'
showMCR: no visible global function definition for 'lines'
showMCR: no visible global function definition for 'median'
showSegment : getMean: no visible global function definition for
'median'
topGenes: no visible global function definition for 'quantile'
Undefined global functions or variables:
CNA approx axis backgroundCorrect box dev.off lines median
normalizeWithinArrays par png points polygon quantile read.maimages
rs segBy segment smooth.CNA
Consider adding
importFrom("grDevices", "dev.off", "png")
importFrom("graphics", "axis", "box", "lines", "par", "points",
"polygon")
importFrom("stats", "approx", "median", "quantile")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'SGOL,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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: 1 WARNING, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/cghMCR.Rcheck/00check.log'
for details.
cghMCR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/cghMCR_1.52.0.tar.gz && rm -rf cghMCR.buildbin-libdir && mkdir cghMCR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cghMCR.buildbin-libdir cghMCR_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL cghMCR_1.52.0.zip && rm cghMCR_1.52.0.tar.gz cghMCR_1.52.0.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
1 36.5M 1 411k 0 0 727k 0 0:00:51 --:--:-- 0:00:51 727k
5 36.5M 5 1941k 0 0 1238k 0 0:00:30 0:00:01 0:00:29 1239k
11 36.5M 11 4380k 0 0 1704k 0 0:00:21 0:00:02 0:00:19 1704k
20 36.5M 20 7778k 0 0 2176k 0 0:00:17 0:00:03 0:00:14 2176k
32 36.5M 32 11.7M 0 0 2624k 0 0:00:14 0:00:04 0:00:10 2624k
39 36.5M 39 14.5M 0 0 2663k 0 0:00:14 0:00:05 0:00:09 2882k
49 36.5M 49 17.9M 0 0 2803k 0 0:00:13 0:00:06 0:00:07 3294k
61 36.5M 61 22.4M 0 0 3036k 0 0:00:12 0:00:07 0:00:05 3720k
76 36.5M 76 27.8M 0 0 3327k 0 0:00:11 0:00:08 0:00:03 4149k
93 36.5M 93 34.1M 0 0 3652k 0 0:00:10 0:00:09 0:00:01 4593k
100 36.5M 100 36.5M 0 0 3768k 0 0:00:09 0:00:09 --:--:-- 5187k
install for i386
* installing *source* package 'cghMCR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'cghMCR'
finding HTML links ... done
SGOL-class html
cghMCR-class html
cghMCR html
mergeMCRProbes html
methods html
plot.DNAcopy 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 'cghMCR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cghMCR' as cghMCR_1.52.0.zip
* DONE (cghMCR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'cghMCR' successfully unpacked and MD5 sums checked
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cghMCR.Rcheck/examples_i386/cghMCR-Ex.timings
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cghMCR.Rcheck/examples_x64/cghMCR-Ex.timings
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