Back to Multiple platform build/check report for BioC 3.8
ABCD[E]FGHIJKLMNOPQRSTUVWXYZ

CHECK report for EnrichedHeatmap on tokay1

This page was generated on 2019-04-13 11:25:55 -0400 (Sat, 13 Apr 2019).

Package 471/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EnrichedHeatmap 1.12.0
Zuguang Gu
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/EnrichedHeatmap
Branch: RELEASE_3_8
Last Commit: 4deed55
Last Changed Date: 2018-10-30 11:41:59 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: EnrichedHeatmap
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EnrichedHeatmap.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings EnrichedHeatmap_1.12.0.tar.gz
StartedAt: 2019-04-13 02:03:29 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:07:11 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 221.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: EnrichedHeatmap.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EnrichedHeatmap.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings EnrichedHeatmap_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/EnrichedHeatmap.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'EnrichedHeatmap/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EnrichedHeatmap' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'EnrichedHeatmap' can be installed ... WARNING
Found the following significant warnings:
  dist_by_closeness.cpp:12:27: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWSNKOW/R.INSTALL24545cae298b/EnrichedHeatmap/man/draw-EnrichedHeatmap-method.rd:16: file link 'draw' in package 'ComplexHeatmap' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWSNKOW/R.INSTALL24545cae298b/EnrichedHeatmap/man/draw-EnrichedHeatmapList-method.rd:18: file link 'make_layout' in package 'ComplexHeatmap' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWSNKOW/R.INSTALL24545cae298b/EnrichedHeatmap/man/draw-EnrichedHeatmapList-method.rd:18: file link 'draw' in package 'ComplexHeatmap' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWSNKOW/R.INSTALL24545cae298b/EnrichedHeatmap/man/draw-EnrichedHeatmapList-method.rd:22: file link 'draw' in package 'ComplexHeatmap' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/EnrichedHeatmap.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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
as.normalizedMatrix: no visible binding for global variable
  'target_is_single_point'
Undefined global functions or variables:
  target_is_single_point
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
EnrichedHeatmap 8.86   0.24    9.53
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
EnrichedHeatmap 9.52   0.23    9.75
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.R'
 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-3.8-bioc/meat/EnrichedHeatmap.Rcheck/00check.log'
for details.



Installation output

EnrichedHeatmap.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/EnrichedHeatmap_1.12.0.tar.gz && rm -rf EnrichedHeatmap.buildbin-libdir && mkdir EnrichedHeatmap.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EnrichedHeatmap.buildbin-libdir EnrichedHeatmap_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL EnrichedHeatmap_1.12.0.zip && rm EnrichedHeatmap_1.12.0.tar.gz EnrichedHeatmap_1.12.0.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 4825k  100 4825k    0     0  40.6M      0 --:--:-- --:--:-- --:--:-- 42.0M

install for i386

* installing *source* package 'EnrichedHeatmap' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c dist_by_closeness.cpp -o dist_by_closeness.o
dist_by_closeness.cpp: In function 'float closeness(Rcpp::NumericVector, Rcpp::NumericVector)':
dist_by_closeness.cpp:12:27: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
    if(std::abs(x1[i] - 0) < 1e-6 | std::abs(x2[j] - 0) < 1e-6) {
                           ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o EnrichedHeatmap.dll tmp.def RcppExports.o dist_by_closeness.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/EnrichedHeatmap.buildbin-libdir/EnrichedHeatmap/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'EnrichedHeatmap'
    finding HTML links ... done
    EnrichedHeatmap-class                   html  
    EnrichedHeatmap                         html  
    EnrichedHeatmapList-class               html  
    EnrichedHeatmapList                     html  
    Extract.normalizedMatrix                html  
    add.AdditiveUnit                        html  
    finding level-2 HTML links ... done

    anno_enriched                           html  
    as.normalizedMatrix                     html  
    copyAttr                                html  
    default_smooth_fun                      html  
    discretize                              html  
    dist_by_closeness                       html  
    draw-EnrichedHeatmap-method             html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWSNKOW/R.INSTALL24545cae298b/EnrichedHeatmap/man/draw-EnrichedHeatmap-method.rd:16: file link 'draw' in package 'ComplexHeatmap' does not exist and so has been treated as a topic
    draw-EnrichedHeatmapList-method         html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWSNKOW/R.INSTALL24545cae298b/EnrichedHeatmap/man/draw-EnrichedHeatmapList-method.rd:18: file link 'make_layout' in package 'ComplexHeatmap' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWSNKOW/R.INSTALL24545cae298b/EnrichedHeatmap/man/draw-EnrichedHeatmapList-method.rd:18: file link 'draw' in package 'ComplexHeatmap' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWSNKOW/R.INSTALL24545cae298b/EnrichedHeatmap/man/draw-EnrichedHeatmapList-method.rd:22: file link 'draw' in package 'ComplexHeatmap' does not exist and so has been treated as a topic
    draw-dispatch                           html  
    enriched_score                          html  
    extract_anno_enriched                   html  
    getSignalsFromList                      html  
    makeWindows                             html  
    normalizeToMatrix                       html  
    print.normalizedMatrix                  html  
    rbind.normalizedMatrix                  html  
    show-EnrichedHeatmap-method             html  
    show-EnrichedHeatmapList-method         html  
    show-dispatch                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'EnrichedHeatmap' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c dist_by_closeness.cpp -o dist_by_closeness.o
dist_by_closeness.cpp: In function 'float closeness(Rcpp::NumericVector, Rcpp::NumericVector)':
dist_by_closeness.cpp:12:27: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
    if(std::abs(x1[i] - 0) < 1e-6 | std::abs(x2[j] - 0) < 1e-6) {
                           ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o EnrichedHeatmap.dll tmp.def RcppExports.o dist_by_closeness.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/EnrichedHeatmap.buildbin-libdir/EnrichedHeatmap/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EnrichedHeatmap' as EnrichedHeatmap_1.12.0.zip
* DONE (EnrichedHeatmap)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'EnrichedHeatmap' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

EnrichedHeatmap.Rcheck/tests_i386/test-all.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> suppressWarnings(suppressPackageStartupMessages(library(EnrichedHeatmap)))
> 
> test_check("EnrichedHeatmap")
== testthat results  ===========================================================
OK: 25 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   8.85    0.26    9.11 

EnrichedHeatmap.Rcheck/tests_x64/test-all.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> suppressWarnings(suppressPackageStartupMessages(library(EnrichedHeatmap)))
> 
> test_check("EnrichedHeatmap")
== testthat results  ===========================================================
OK: 25 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   9.50    0.21    9.70 

Example timings

EnrichedHeatmap.Rcheck/examples_i386/EnrichedHeatmap-Ex.timings

nameusersystemelapsed
EnrichedHeatmap-class000
EnrichedHeatmap8.860.249.53
EnrichedHeatmapList-class000
EnrichedHeatmapList000
Extract.normalizedMatrix000
add.AdditiveUnit000
anno_enriched3.420.063.48
as.normalizedMatrix000
copyAttr0.280.000.28
default_smooth_fun000
discretize000
dist_by_closeness000
draw-EnrichedHeatmap-method000
draw-EnrichedHeatmapList-method000
draw-dispatch000
enriched_score000
extract_anno_enriched000
getSignalsFromList000
makeWindows0.150.000.16
normalizeToMatrix2.390.002.39
print.normalizedMatrix000
rbind.normalizedMatrix000
show-EnrichedHeatmap-method000
show-EnrichedHeatmapList-method000
show-dispatch000

EnrichedHeatmap.Rcheck/examples_x64/EnrichedHeatmap-Ex.timings

nameusersystemelapsed
EnrichedHeatmap-class000
EnrichedHeatmap9.520.239.75
EnrichedHeatmapList-class000
EnrichedHeatmapList000
Extract.normalizedMatrix000
add.AdditiveUnit000
anno_enriched3.890.194.08
as.normalizedMatrix000
copyAttr0.360.000.36
default_smooth_fun000
discretize000
dist_by_closeness0.010.000.02
draw-EnrichedHeatmap-method000
draw-EnrichedHeatmapList-method000
draw-dispatch000
enriched_score000
extract_anno_enriched000
getSignalsFromList000
makeWindows0.190.000.18
normalizeToMatrix3.170.003.18
print.normalizedMatrix000
rbind.normalizedMatrix000
show-EnrichedHeatmap-method000
show-EnrichedHeatmapList-method000
show-dispatch000