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CHECK report for HMMcopy on malbec1

This page was generated on 2021-05-06 12:27:53 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the HMMcopy package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 844/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HMMcopy 1.32.0  (landing page)
Daniel Lai , Sohrab Shah
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/HMMcopy
Branch: RELEASE_3_12
Last Commit: ba30e1f
Last Changed Date: 2020-10-27 10:47:39 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: HMMcopy
Version: 1.32.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:HMMcopy.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings HMMcopy_1.32.0.tar.gz
StartedAt: 2021-05-06 02:29:29 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:30:01 -0400 (Thu, 06 May 2021)
EllapsedTime: 32.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: HMMcopy.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:HMMcopy.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings HMMcopy_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/HMMcopy.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HMMcopy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HMMcopy’ version ‘1.32.0’
* 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 ‘HMMcopy’ 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 ... 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 ... WARNING
Missing link or links in documentation object 'HMMcopy-dataset.Rd':
  ‘[IRanges:RangedData-class]{RangedData}’

Missing link or links in documentation object 'HMMcopy-input.Rd':
  ‘[IRanges:RangedData-class]{RangedData}’

Missing link or links in documentation object 'HMMcopy-output.Rd':
  ‘[IRanges:RangedData-class]{RangedData}’

Missing link or links in documentation object 'correctReadcount.Rd':
  ‘[IRanges:RangedData-class]{RangedData}’

Missing link or links in documentation object 'wigsToRangedData.Rd':
  ‘[IRanges:RangedData-class]{RangedData}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
HMMcopy-package 5.756  0.104   5.879
* 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
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/HMMcopy.Rcheck/00check.log’
for details.



Installation output

HMMcopy.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL HMMcopy
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘HMMcopy’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c forward_backward.c -o forward_backward.o
forward_backward.c: In function ‘forward_backward’:
forward_backward.c:28:13: warning: unused variable ‘tmp’ [-Wunused-variable]
   int K, T, tmp;
             ^~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c register.c -o register.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c viterbi.c -o viterbi.o
viterbi.c: In function ‘viterbi’:
viterbi.c:21:13: warning: unused variable ‘tmp’ [-Wunused-variable]
   int K, T, tmp;
             ^~~
gcc -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o HMMcopy.so forward_backward.o register.o viterbi.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-HMMcopy/00new/HMMcopy/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 (HMMcopy)

Tests output


Example timings

HMMcopy.Rcheck/HMMcopy-Ex.timings

nameusersystemelapsed
HMMcopy-input0.0520.0000.053
HMMcopy-output0.1960.0280.224
HMMcopy-package5.7560.1045.879
HMMcopy-visualize2.2040.0242.237
HMMsegment0.1760.0040.183
correctReadcount0.1480.0000.149
wigsToRangedData0.0680.0000.069