Mark van de Wiel
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/CGHbase |
| git_branch: RELEASE_3_13 |
| git_last_commit: 25d9f08 |
| git_last_commit_date: 2021-05-19 11:40:57 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:00 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the CGHbase package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CGHbase.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 278/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CGHbase 1.52.0 (landing page) Mark van de Wiel
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CGHbase |
| Version: 1.52.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CGHbase.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CGHbase_1.52.0.tar.gz |
| StartedAt: 2021-10-14 20:54:17 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 20:55:26 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 69.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CGHbase.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CGHbase.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CGHbase_1.52.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CGHbase.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CGHbase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CGHbase' 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 'CGHbase' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
Package in Depends field not imported from: 'methods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
':::' call which should be '::': 'Biobase:::assayDataElement'
See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'Biobase:::assayDataDims'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.makeEmptyFeatureData: no visible global function definition for 'is'
.makeEmptyFeatureData: no visible global function definition for 'new'
.makeEmptyFeatureDataForRegions: no visible global function definition
for 'is'
.makeEmptyFeatureDataForRegions: no visible global function definition
for 'new'
frequencyPlotCalls: no visible global function definition for 'rect'
frequencyPlotCalls: no visible global function definition for 'box'
frequencyPlotCalls: no visible global function definition for 'abline'
frequencyPlotCalls: no visible global function definition for 'axis'
frequencyPlotCalls: no visible global function definition for 'mtext'
frequencyPlotCalls: no visible global function definition for 'median'
make_cghRaw: no visible global function definition for 'read.table'
make_cghRaw: no visible global function definition for 'new'
summaryPlot: no visible global function definition for 'rect'
summaryPlot: no visible global function definition for 'box'
summaryPlot: no visible global function definition for 'abline'
summaryPlot: no visible global function definition for 'axis'
summaryPlot: no visible global function definition for 'mtext'
summaryPlot: no visible global function definition for 'median'
frequencyPlot,cghRegions-missing: no visible global function definition
for 'par'
frequencyPlot,cghRegions-missing: no visible global function definition
for 'barplot'
frequencyPlot,cghRegions-missing: no visible global function definition
for 'segments'
frequencyPlot,cghRegions-missing: no visible global function definition
for 'gray'
frequencyPlot,cghRegions-missing: no visible global function definition
for 'box'
frequencyPlot,cghRegions-missing: no visible global function definition
for 'axis'
initialize,cghCall: no visible global function definition for 'new'
initialize,cghCall: no visible global function definition for
'callNextMethod'
initialize,cghRaw: no visible global function definition for 'new'
initialize,cghRaw: no visible global function definition for
'callNextMethod'
initialize,cghRegions: no visible global function definition for 'new'
initialize,cghRegions: no visible global function definition for
'callNextMethod'
initialize,cghSeg: no visible global function definition for 'new'
initialize,cghSeg: no visible global function definition for
'callNextMethod'
plot.cghRegions,cghRegions-missing: no visible global function
definition for 'layout'
plot.cghRegions,cghRegions-missing: no visible global function
definition for 'par'
plot.cghRegions,cghRegions-missing: no visible global function
definition for 'segments'
plot.cghRegions,cghRegions-missing: no visible global function
definition for 'axis'
plot,cghCall-missing: no visible global function definition for 'par'
plot,cghCall-missing: no visible global function definition for 'rect'
plot,cghCall-missing: no visible global function definition for 'axis'
plot,cghCall-missing: no visible global function definition for 'box'
plot,cghCall-missing: no visible global function definition for
'abline'
plot,cghCall-missing: no visible global function definition for 'mtext'
plot,cghCall-missing: no visible global function definition for 'title'
plot,cghCall-missing: no visible global function definition for
'segments'
plot,cghCall-missing: no visible global function definition for
'median'
plot,cghCall-missing : <anonymous>: no visible global function
definition for 'mad'
plot,cghRaw-missing: no visible global function definition for 'mtext'
plot,cghRaw-missing: no visible global function definition for 'abline'
plot,cghRaw-missing: no visible global function definition for 'axis'
plot,cghRaw-missing: no visible global function definition for 'median'
plot,cghRaw-missing : <anonymous>: no visible global function
definition for 'mad'
plot,cghSeg-missing: no visible global function definition for 'mtext'
plot,cghSeg-missing: no visible global function definition for 'abline'
plot,cghSeg-missing: no visible global function definition for 'axis'
plot,cghSeg-missing: no visible global function definition for
'segments'
plot,cghSeg-missing: no visible global function definition for 'median'
plot,cghSeg-missing : <anonymous>: no visible global function
definition for 'mad'
Undefined global functions or variables:
abline axis barplot box callNextMethod gray is layout mad median
mtext new par read.table rect segments title
Consider adding
importFrom("grDevices", "gray")
importFrom("graphics", "abline", "axis", "barplot", "box", "layout",
"mtext", "par", "rect", "segments", "title")
importFrom("methods", "callNextMethod", "is", "new")
importFrom("stats", "mad", "median")
importFrom("utils", "read.table")
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 examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/CGHbase.Rcheck/00check.log'
for details.
CGHbase.Rcheck/00install.out
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### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CGHbase_1.52.0.tar.gz && rm -rf CGHbase.buildbin-libdir && mkdir CGHbase.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CGHbase.buildbin-libdir CGHbase_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CGHbase_1.52.0.zip && rm CGHbase_1.52.0.tar.gz CGHbase_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
100 847k 100 847k 0 0 1725k 0 --:--:-- --:--:-- --:--:-- 1730k
install for i386
* installing *source* package 'CGHbase' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CGHbase'
finding HTML links ... done
CGHbase-package html
Wilting html
WiltingCalled html
WiltingNorm html
WiltingRaw html
WiltingRegions html
WiltingSeg html
avedist html
chromosomes html
class.cghCall html
class.cghRaw html
class.cghRegions html
class.cghSeg html
copynumber html
frequencyPlot html
frequencyPlotCalls html
make_cghRaw html
plot html
probloss html
regions html
summaryPlot html
** building package indices
** 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 'CGHbase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CGHbase' as CGHbase_1.52.0.zip
* DONE (CGHbase)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CGHbase' successfully unpacked and MD5 sums checked
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CGHbase.Rcheck/examples_i386/CGHbase-Ex.timings
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CGHbase.Rcheck/examples_x64/CGHbase-Ex.timings
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