Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-27 11:05:40 -0500 (Thu, 27 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
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

CHECK results for exomeCopy on nebbiolo1


To the developers/maintainers of the exomeCopy package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/exomeCopy.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.

raw results

Package 612/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
exomeCopy 1.41.1  (landing page)
Michael Love
Snapshot Date: 2022-01-26 13:55:18 -0500 (Wed, 26 Jan 2022)
git_url: https://git.bioconductor.org/packages/exomeCopy
git_branch: master
git_last_commit: 953e9d0
git_last_commit_date: 2021-11-20 04:00:19 -0500 (Sat, 20 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'IRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: exomeCopy
Version: 1.41.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:exomeCopy.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings exomeCopy_1.41.1.tar.gz
StartedAt: 2022-01-26 19:14:18 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 19:15:51 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 93.3 seconds
RetCode: 0
Status:   OK  
CheckDir: exomeCopy.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:exomeCopy.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings exomeCopy_1.41.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/exomeCopy.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘exomeCopy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘exomeCopy’ version ‘1.41.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘exomeCopy’ can be installed ... OK
* checking installed package size ... OK
* 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
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.ExomeCopy
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
emFn : <anonymous>: no visible global function definition for ‘dnbinom’
exomeCopy: no visible global function definition for ‘lm’
exomeCopy: no visible global function definition for ‘optim’
exomeCopy: no visible global function definition for ‘new’
exomeCopy: no visible global function definition for ‘Rle’
getGCcontent: no visible global function definition for
  ‘letterFrequency’
plot.ExomeCopy: no visible global function definition for ‘segments’
plot.ExomeCopy: no visible global function definition for ‘legend’
plotCompiledCNV: no visible global function definition for ‘axis’
plotCompiledCNV: no visible global function definition for ‘segments’
plot,ExomeCopy-missing: no visible global function definition for
  ‘segments’
plot,ExomeCopy-missing: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  Rle axis dnbinom legend letterFrequency lm new optim segments
Consider adding
  importFrom("graphics", "axis", "legend", "segments")
  importFrom("methods", "new")
  importFrom("stats", "dnbinom", "lm", "optim")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/exomeCopy.Rcheck/00check.log’
for details.



Installation output

exomeCopy.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL exomeCopy
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘exomeCopy’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c exomeCopy.c -o exomeCopy.o
gcc -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o exomeCopy.so exomeCopy.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-exomeCopy/00new/exomeCopy/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (exomeCopy)

Tests output


Example timings

exomeCopy.Rcheck/exomeCopy-Ex.timings

nameusersystemelapsed
ExomeCopy-class0.0020.0000.002
compileCopyCountSegments2.8220.0762.899
copyCountSegments2.2420.0002.242
countBamInGRanges0.2560.0120.268
exomeCopy2.1470.0122.160
generateBackground0.1290.0000.129
getGCcontent0.0170.0000.018
negLogLike0.0090.0000.009
plot.exomeCopyObject2.3090.0042.315
plotCompiledCNV2.6960.0042.700
subdivideGRanges0.0640.0000.064