Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-03 13:04:47 -0500 (Fri, 03 Dec 2021).

CHECK results for DSS on nebbiolo2

To the developers/maintainers of the DSS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DSS.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 546/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DSS 2.42.0  (landing page)
Hao Wu , Hao Feng
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/DSS
git_branch: RELEASE_3_14
git_last_commit: 33e8745
git_last_commit_date: 2021-10-26 12:03:27 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: DSS
Version: 2.42.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:DSS.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings DSS_2.42.0.tar.gz
StartedAt: 2021-12-02 07:02:14 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 07:06:02 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 228.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DSS.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:DSS.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings DSS_2.42.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/DSS.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DSS/DESCRIPTION’ ... OK
* this is package ‘DSS’ version ‘2.42.0’
* 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 ‘DSS’ 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 ... WARNING
'::' or ':::' import not declared from: ‘matrixStats’
Namespace in Imports field not imported from: ‘DelayedArray’
  All declared Imports should be used.
* 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 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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/DSS.Rcheck/00check.log’
for details.



Installation output

DSS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL DSS
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘DSS’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c compute_var_smooth.c -o compute_var_smooth.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c filter.c -o filter.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c nitem.c -o nitem.o
gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o DSS.so compute_var_smooth.o filter.o nitem.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-DSS/00new/DSS/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 (DSS)

Tests output


Example timings

DSS.Rcheck/DSS-Ex.timings

nameusersystemelapsed
DMLfit.multiFactor000
DMLtest0.0010.0000.001
DMLtest.multiFactor000
DSS.DE0.2000.0080.208
RRBS0.0280.0040.032
SeqCountSet-class0.1690.0280.198
callDML0.0010.0000.001
callDMR000
design0.0240.0000.024
dispersion0.0760.0120.088
estDispersion0.3670.0000.367
estNormFactors0.0110.0000.012
makeBSseqData1.8700.0351.906
normalizationFactor0.0050.0010.004
seqData0.0040.0000.003
showOneDMR000
waldTest0.0720.0000.072