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This page was generated on 2023-03-22 11:05:00 -0400 (Wed, 22 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4271
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4214
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4259
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 DegNorm on nebbiolo2


To the developers/maintainers of the DegNorm package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DegNorm.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 499/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DegNorm 1.8.2  (landing page)
Ji-Ping Wang
Snapshot Date: 2023-03-20 14:00:04 -0400 (Mon, 20 Mar 2023)
git_url: https://git.bioconductor.org/packages/DegNorm
git_branch: RELEASE_3_16
git_last_commit: cfa5bdd
git_last_commit_date: 2023-01-19 11:15:53 -0400 (Thu, 19 Jan 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DegNorm
Version: 1.8.2
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:DegNorm.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings DegNorm_1.8.2.tar.gz
StartedAt: 2023-03-20 20:15:13 -0400 (Mon, 20 Mar 2023)
EndedAt: 2023-03-20 20:22:34 -0400 (Mon, 20 Mar 2023)
EllapsedTime: 440.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DegNorm.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:DegNorm.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings DegNorm_1.8.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/DegNorm.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘DegNorm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DegNorm’ version ‘1.8.2’
* 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 ‘DegNorm’ can be installed ... 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 loading without being on the library search path ... WARNING
Error in library(DegNorm, lib.loc = "/home/biocbuild/bbs-3.16-bioc/R/library") : 
  there is no package called ‘DegNorm’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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 ... OK
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘DegNorm.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/DegNorm.Rcheck/00check.log’
for details.



Installation output

DegNorm.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL DegNorm
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘DegNorm’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I/usr/local/include  -fopenmp  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/IRanges/include' -I/usr/local/include  -fopenmp  -fpic  -g -O2  -Wall -c degnormCPP.cpp -o degnormCPP.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o DegNorm.so RcppExports.o degnormCPP.o -fopenmp -L/home/biocbuild/bbs-3.16-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.16-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-DegNorm/00new/DegNorm/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 (DegNorm)

Tests output


Example timings