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This page was generated on 2022-01-21 13:06:15 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 tokay2


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: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
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 20.04.4 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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DSS.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DSS_2.42.0.tar.gz
StartedAt: 2022-01-20 19:09:29 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 19:15:10 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 340.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DSS.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DSS.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DSS_2.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/DSS.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/DSS/libs/i386/DSS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/DSS/libs/x64/DSS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/DSS.Rcheck/00check.log'
for details.



Installation output

DSS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/DSS_2.42.0.tar.gz && rm -rf DSS.buildbin-libdir && mkdir DSS.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DSS.buildbin-libdir DSS_2.42.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL DSS_2.42.0.zip && rm DSS_2.42.0.tar.gz DSS_2.42.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1152k  100 1152k    0     0  1924k      0 --:--:-- --:--:-- --:--:-- 1926k

install for i386

* installing *source* package 'DSS' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c compute_var_smooth.c -o compute_var_smooth.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c filter.c -o filter.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c nitem.c -o nitem.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o DSS.dll tmp.def compute_var_smooth.o filter.o nitem.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/DSS.buildbin-libdir/00LOCK-DSS/00new/DSS/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DSS'
    finding HTML links ... done
    DMLfit.multiFactor                      html  
    DMLtest                                 html  
    DMLtest.multiFactor                     html  
    DSS-package                             html  
    DSS.DE                                  html  
    RRBS                                    html  
    SeqCountSet-class                       html  
    finding level-2 HTML links ... done

    callDML                                 html  
    callDMR                                 html  
    design                                  html  
    dispersion                              html  
    estDispersion                           html  
    estNormFactors                          html  
    makeBSseqData                           html  
    normalizationFactor                     html  
    seqData                                 html  
    showOneDMR                              html  
    waldTest                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'DSS' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c compute_var_smooth.c -o compute_var_smooth.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c filter.c -o filter.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c nitem.c -o nitem.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o DSS.dll tmp.def compute_var_smooth.o filter.o nitem.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/DSS.buildbin-libdir/DSS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DSS' as DSS_2.42.0.zip
* DONE (DSS)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'DSS' successfully unpacked and MD5 sums checked

Tests output


Example timings

DSS.Rcheck/examples_i386/DSS-Ex.timings

nameusersystemelapsed
DMLfit.multiFactor000
DMLtest000
DMLtest.multiFactor000
DSS.DE0.160.030.19
RRBS0.010.030.05
SeqCountSet-class0.170.080.25
callDML000
callDMR000
design0.040.000.03
dispersion0.210.030.25
estDispersion0.210.030.23
estNormFactors0.000.020.02
makeBSseqData1.650.061.95
normalizationFactor0.020.000.02
seqData0.010.000.01
showOneDMR000
waldTest0.110.000.11

DSS.Rcheck/examples_x64/DSS-Ex.timings

nameusersystemelapsed
DMLfit.multiFactor000
DMLtest000
DMLtest.multiFactor000
DSS.DE0.200.030.23
RRBS0.020.010.03
SeqCountSet-class0.200.020.22
callDML000
callDMR000
design0.050.000.05
dispersion0.140.000.15
estDispersion0.340.030.38
estNormFactors0.030.000.03
makeBSseqData1.660.021.67
normalizationFactor000
seqData0.000.010.02
showOneDMR000
waldTest0.170.000.17