Yuzhu Duan
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/signatureSearch |
| Branch: RELEASE_3_10 |
| Last Commit: 712e3fb |
| Last Changed Date: 2020-04-06 14:01:21 -0400 (Mon, 06 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:33:39 -0400 (Wed, 15 Apr 2020).
| Package 1589/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| signatureSearch 1.0.4 Yuzhu Duan
| malbec1 | Linux (Ubuntu 18.04.4 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 | WARNINGS | OK | |
| Package: signatureSearch |
| Version: 1.0.4 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:signatureSearch.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings signatureSearch_1.0.4.tar.gz |
| StartedAt: 2020-04-15 06:40:37 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:46:58 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 381.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: signatureSearch.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:signatureSearch.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings signatureSearch_1.0.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/signatureSearch.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 'signatureSearch/DESCRIPTION' ... OK
* this is package 'signatureSearch' version '1.0.4'
* 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 ... NOTE
Found the following hidden files and directories:
inst/extdata/.batchtools.conf.R
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'signatureSearch' 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 ... WARNING
Undocumented code objects:
'runWF' 'tarReduce' 'vec_char_redu'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 R/sysdata.rda ... 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/signatureSearch/libs/i386/signatureSearch.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/signatureSearch/libs/x64/signatureSearch.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
dtnetplot 4.45 1.51 6.73
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
dtnetplot 6.80 1.11 8.2
rand_query_ES 4.25 0.08 5.8
* 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 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/signatureSearch.Rcheck/00check.log'
for details.
signatureSearch.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/signatureSearch_1.0.4.tar.gz && rm -rf signatureSearch.buildbin-libdir && mkdir signatureSearch.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=signatureSearch.buildbin-libdir signatureSearch_1.0.4.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL signatureSearch_1.0.4.zip && rm signatureSearch_1.0.4.tar.gz signatureSearch_1.0.4.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 1634k 100 1634k 0 0 15.7M 0 --:--:-- --:--:-- --:--:-- 16.2M
install for i386
* installing *source* package 'signatureSearch' ...
** 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 fastGSEA.cpp -o fastGSEA.o
fastGSEA.cpp: In function 'Rcpp::NumericVector calcGseaStatBatchCpp(const NumericVector&, const List&, const IntegerVector&)':
fastGSEA.cpp:444:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < S.size(); ++j) {
^
C:/Rtools/mingw_32/bin/gcc -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" -O3 -Wall -std=gnu99 -mtune=core2 -c fgsea_init.c -o fgsea_init.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o signatureSearch.dll tmp.def RcppExports.o fastGSEA.o fgsea_init.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/signatureSearch.buildbin-libdir/00LOCK-signatureSearch/00new/signatureSearch/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'signatureSearch'
finding HTML links ... done
GCT-object html
append2H5 html
build_custom_db html
cell_info html
chembl_moa_list html
clue_moa_list html
comp_fea_res html
create_empty_h5 html
dim-methods html
drug_cell_ranks html
drugs-methods html
drugs10 html
dsea_GSEA html
dsea_hyperG html
dtnetplot html
enrichGO2 html
enrichKEGG2 html
enrichMOA html
feaResult-class html
feaResult html
gctx2h5 html
gessResult-class html
gessResult html
gess_cmap html
gess_cor html
gess_fisher html
gess_gcmap html
gess_lincs html
gess_res_vis html
getSig html
get_targets html
gseGO2 html
gseKEGG2 html
head-methods html
mabsGO html
mabsKEGG html
matrix2h5 html
moa_conn html
parse_gctx html
qSig-class html
qSig html
rand_query_ES html
result-methods html
show-methods html
signatureSearch-package html
sim_score_grp html
tail-methods html
targetList html
tsea_dup_hyperG html
tsea_mGSEA html
tsea_mabs 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 'signatureSearch' ...
** 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 fastGSEA.cpp -o fastGSEA.o
fastGSEA.cpp: In function 'Rcpp::NumericVector calcGseaStatBatchCpp(const NumericVector&, const List&, const IntegerVector&)':
fastGSEA.cpp:444:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < S.size(); ++j) {
^
C:/Rtools/mingw_64/bin/gcc -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 -std=gnu99 -mtune=core2 -c fgsea_init.c -o fgsea_init.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o signatureSearch.dll tmp.def RcppExports.o fastGSEA.o fgsea_init.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/signatureSearch.buildbin-libdir/signatureSearch/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'signatureSearch' as signatureSearch_1.0.4.zip
* DONE (signatureSearch)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'signatureSearch' successfully unpacked and MD5 sums checked
|
signatureSearch.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(signatureSearch)
> #
> # test_check("signatureSearch")
>
> proc.time()
user system elapsed
0.14 0.03 0.15
|
signatureSearch.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(signatureSearch)
> #
> # test_check("signatureSearch")
>
> proc.time()
user system elapsed
0.20 0.00 0.18
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signatureSearch.Rcheck/examples_i386/signatureSearch-Ex.timings
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signatureSearch.Rcheck/examples_x64/signatureSearch-Ex.timings
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