Chengyang Ji
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/sitePath |
| Branch: RELEASE_3_10 |
| Last Commit: 86e44d4 |
| Last Changed Date: 2020-04-01 12:28:39 -0400 (Wed, 01 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:32:11 -0400 (Wed, 15 Apr 2020).
| Package 1609/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| sitePath 1.2.3 Chengyang Ji
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: sitePath |
| Version: 1.2.3 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sitePath.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings sitePath_1.2.3.tar.gz |
| StartedAt: 2020-04-15 06:42:48 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:50:42 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 473.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sitePath.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sitePath.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings sitePath_1.2.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/sitePath.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sitePath/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sitePath' version '1.2.3'
* 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 whether package 'sitePath' 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 ... 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 ... 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-3.10-bioc/R/library/sitePath/libs/i386/sitePath.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/sitePath/libs/x64/sitePath.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
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
Examples with CPU or elapsed time > 5s
user system elapsed
pre-assessment 7.85 0.05 7.89
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
pre-assessment 8.02 0.02 8.04
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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 NOTE
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/sitePath.Rcheck/00check.log'
for details.
sitePath.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/sitePath_1.2.3.tar.gz && rm -rf sitePath.buildbin-libdir && mkdir sitePath.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sitePath.buildbin-libdir sitePath_1.2.3.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL sitePath_1.2.3.zip && rm sitePath_1.2.3.tar.gz sitePath_1.2.3.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 179k 100 179k 0 0 4493k 0 --:--:-- --:--:-- --:--:-- 4985k
install for i386
* installing *source* package 'sitePath' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c exportFunc.cpp -o exportFunc.o
exportFunc.cpp: In function 'Rcpp::ListOf<Rcpp::Vector<13> > majorSNPtips(const CharacterVector&, int)':
exportFunc.cpp:54:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int siteIndex = 0; siteIndex < alignedSeqs[0].size(); ++siteIndex) {
^
exportFunc.cpp: In function 'Rcpp::ListOf<Rcpp::Vector<13> > mergePaths(const Rcpp::ListOf<Rcpp::Vector<13> >&)':
exportFunc.cpp:85:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int i = 1; i < paths.size(); ++i) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c minEntropy.cpp -o minEntropy.o
minEntropy.cpp: In function 'Rcpp::ListOf<Rcpp::Vector<13> > MinEntropy::updatedSegmentation(const Rcpp::ListOf<Rcpp::Vector<13> >&, const segment&)':
minEntropy.cpp:389:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int j = 0; j < aa.size(); ++j) {
^
minEntropy.cpp: In instantiation of 'MinEntropy::SearchTree<T>::SearchTree(unsigned int, unsigned int, const Rcpp::ListOf<Rcpp::Vector<13> >&) [with T = MinEntropy::Segmentor]':
minEntropy.cpp:438:28: required from here
minEntropy.cpp:177:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int j = 0; j < aa.size(); ++j) {
^
minEntropy.cpp: In instantiation of 'MinEntropy::SearchTree<T>::SearchTree(unsigned int, unsigned int, const Rcpp::ListOf<Rcpp::Vector<13> >&) [with T = MinEntropy::Amalgamator]':
minEntropy.cpp:439:28: required from here
minEntropy.cpp:177:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c treemer.cpp -o treemer.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c util.cpp -o util.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o sitePath.dll tmp.def RcppExports.o exportFunc.o minEntropy.o treemer.o util.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/sitePath.buildbin-libdir/00LOCK-sitePath/00new/sitePath/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'sitePath'
finding HTML links ... done
addMSA html
extractTips html
findSites html
h3n2_align html
h3n2_align_reduced html
h3n2_tree html
h3n2_tree_reduced html
plot.lineagePath html
plot.sitePath html
plotSingleSite html
pre-assessment html
setSiteNumbering html
treemer html
zikv_align html
zikv_align_reduced html
zikv_tree html
zikv_tree_reduced 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 'sitePath' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c exportFunc.cpp -o exportFunc.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c minEntropy.cpp -o minEntropy.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c treemer.cpp -o treemer.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c util.cpp -o util.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o sitePath.dll tmp.def RcppExports.o exportFunc.o minEntropy.o treemer.o util.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/sitePath.buildbin-libdir/sitePath/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sitePath' as sitePath_1.2.3.zip
* DONE (sitePath)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'sitePath' successfully unpacked and MD5 sums checked
|
sitePath.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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)
> library(sitePath)
>
> test_check("sitePath")
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== testthat results ===========================================================
[ OK: 4346 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
195.17 0.43 195.62
|
sitePath.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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)
> library(sitePath)
>
> test_check("sitePath")
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== testthat results ===========================================================
[ OK: 4330 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
187.48 0.35 187.85
|
|
sitePath.Rcheck/examples_i386/sitePath-Ex.timings
|
sitePath.Rcheck/examples_x64/sitePath-Ex.timings
|