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This page was generated on 2022-06-27 11:05:19 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
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 gcrma on nebbiolo2


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

raw results

Package 720/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gcrma 2.69.0  (landing page)
Z. Wu
Snapshot Date: 2022-06-26 14:00:03 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/gcrma
git_branch: master
git_last_commit: b905c51
git_last_commit_date: 2022-04-26 10:55:00 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: gcrma
Version: 2.69.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:gcrma.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings gcrma_2.69.0.tar.gz
StartedAt: 2022-06-26 19:50:56 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 19:52:33 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 97.3 seconds
RetCode: 0
Status:   OK  
CheckDir: gcrma.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:gcrma.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings gcrma_2.69.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/gcrma.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gcrma/DESCRIPTION’ ... OK
* this is package ‘gcrma’ version ‘2.69.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘gcrma’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘affy’ ‘splines’
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
* 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 ... NOTE
Foreign function call to a different package:
  .Call("rma_c_complete", ..., PACKAGE = "affy")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
compute.affinities: no visible binding for global variable
  ‘affinity.spline.coefs’
compute.affinities.nomm: no visible binding for global variable
  ‘affinity.spline.coefs’
compute.affinities2: no visible binding for global variable
  ‘affinity.spline.coefs’
Undefined global functions or variables:
  affinity.spline.coefs
* 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
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
bg.adjust.gcrma 13.989  0.520  14.509
gcrma           10.545  0.285  10.829
* 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
  ‘/home/biocbuild/bbs-3.16-bioc/meat/gcrma.Rcheck/00check.log’
for details.



Installation output

gcrma.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL gcrma
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘gcrma’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c baseProfile.c -o baseProfile.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c computeAffinities.c -o computeAffinities.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c postmean.c -o postmean.o
gcc -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o gcrma.so baseProfile.o computeAffinities.o postmean.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/library/00LOCK-gcrma/00new/gcrma/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 (gcrma)

Tests output


Example timings

gcrma.Rcheck/gcrma-Ex.timings

nameusersystemelapsed
bg.adjust.gcrma13.989 0.52014.509
gcrma10.545 0.28510.829