Back to Multiple platform build/check report for BioC 3.16:   simplified   long
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-04-12 11:05:03 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 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? 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 575/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DSS 2.46.0  (landing page)
Hao Wu , Hao Feng
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/DSS
git_branch: RELEASE_3_16
git_last_commit: 1b095bf
git_last_commit_date: 2022-12-22 20:59:37 -0400 (Thu, 22 Dec 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  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: DSS
Version: 2.46.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:DSS.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings DSS_2.46.0.tar.gz
StartedAt: 2023-04-10 20:26:43 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 20:31:04 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 260.6 seconds
RetCode: 0
Status:   OK  
CheckDir: DSS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:DSS.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings DSS_2.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/DSS.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 ‘DSS/DESCRIPTION’ ... OK
* this is package ‘DSS’ version ‘2.46.0’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DMLtest: no visible global function definition for ‘detectCores’
dispersion.shrinkage.BSseq: no visible global function definition for
  ‘mclapply’
est.phi.naive: no visible global function definition for ‘rowVars’
est.prior.BSseq.logN: no visible global function definition for
  ‘rowVars’
Undefined global functions or variables:
  detectCores mclapply rowVars
* 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 ...
  ‘DSS.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/DSS.Rcheck/00check.log’
for details.



Installation output

DSS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL DSS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘DSS’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c filter.c -o filter.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c nitem.c -o nitem.o
gcc -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o DSS.so compute_var_smooth.o filter.o nitem.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-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
DMLtest000
DMLtest.multiFactor000
DSS.DE0.1750.0440.218
RRBS0.0230.0000.023
SeqCountSet-class1.1040.1121.216
callDML000
callDMR000
design0.0140.0030.017
dispersion0.0700.0030.073
estDispersion0.2150.0120.229
estNormFactors0.0070.0040.011
makeBSseqData0.6860.0160.702
normalizationFactor0.0030.0000.003
seqData0.0030.0000.003
showOneDMR000
waldTest0.0700.0000.069