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) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:25:55 -0400 (Sat, 13 Apr 2019).
| Package 471/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| EnrichedHeatmap 1.12.0 Zuguang Gu
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| 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 |
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### Running command:
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### 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
###
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* 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.
EnrichedHeatmap.Rcheck/00install.out
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###
### 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
###
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% 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
|
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
|
|
EnrichedHeatmap.Rcheck/examples_i386/EnrichedHeatmap-Ex.timings
|
EnrichedHeatmap.Rcheck/examples_x64/EnrichedHeatmap-Ex.timings
|