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CHECK report for gpart on merida1

This page was generated on 2019-04-16 12:12:41 -0400 (Tue, 16 Apr 2019).

Package 673/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gpart 1.0.3
Sun Ah Kim
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/gpart
Branch: RELEASE_3_8
Last Commit: 7fdaae0
Last Changed Date: 2019-03-31 23:40:23 -0400 (Sun, 31 Mar 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: gpart
Version: 1.0.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gpart.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gpart_1.0.3.tar.gz
StartedAt: 2019-04-16 00:22:50 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:27:09 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 259.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: gpart.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gpart.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gpart_1.0.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/gpart.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gpart/DESCRIPTION’ ... OK
* this is package ‘gpart’ version ‘1.0.3’
* package encoding: UTF-8
* 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 ‘gpart’ can be installed ... WARNING
Found the following significant warnings:
  gpart_cpp.cpp:501:45: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  gpart_cpp.cpp:501:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  gpart_cpp.cpp:561:43: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  gpart_cpp.cpp:561:57: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Users/biocbuild/bbs-3.8-bioc/meat/gpart.Rcheck/00install.out’ for details.
* 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: ‘r.hg38.knownGene’
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/gpart.Rcheck/00check.log’
for details.



Installation output

gpart.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gpart
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘gpart’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c gpart_cpp.cpp -o gpart_cpp.o
gpart_cpp.cpp:501:45: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
          Dpclass = CIDp_strLD(b1, b2,lower = lower, upper=upper);
                                      ˜˜˜˜˜ ^ ˜˜˜˜˜
gpart_cpp.cpp:501:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
          Dpclass = CIDp_strLD(b1, b2,lower = lower, upper=upper);
                                                     ˜˜˜˜˜^˜˜˜˜˜
gpart_cpp.cpp:561:43: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
        Dpclass = CIDp_strLD(b1, b2,lower = lower, upper=upper);
                                    ˜˜˜˜˜ ^ ˜˜˜˜˜
gpart_cpp.cpp:561:57: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
        Dpclass = CIDp_strLD(b1, b2,lower = lower, upper=upper);
                                                   ˜˜˜˜˜^˜˜˜˜˜
4 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o gpart.so RcppExports.o gpart_cpp.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/gpart/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gpart)

Tests output


Example timings

gpart.Rcheck/gpart-Ex.timings

nameusersystemelapsed
BigLD0.1660.0220.188
CLQD0.2950.0160.312
GPART0.7280.0150.748
LDblockHeatmap0.7480.0690.786
convert2GRange0.0840.0020.086