Yuzhu Duan
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/signatureSearch |
| Branch: RELEASE_3_12 |
| Last Commit: 0befcb1 |
| Last Changed Date: 2021-04-23 09:29:56 -0400 (Fri, 23 Apr 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:36:49 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the signatureSearch package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1706/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| signatureSearch 1.4.6 (landing page) Yuzhu Duan
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: signatureSearch |
| Version: 1.4.6 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings signatureSearch_1.4.6.tar.gz |
| StartedAt: 2021-05-06 06:14:56 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:22:04 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 427.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: signatureSearch.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings signatureSearch_1.4.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/signatureSearch.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘signatureSearch/DESCRIPTION’ ... OK
* this is package ‘signatureSearch’ version ‘1.4.6’
* 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 for sufficient/correct file permissions ... 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
* 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 R/sysdata.rda ... 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runWF 60.027 1.364 69.526
set_readable 31.869 1.182 33.540
dtnetplot 7.224 0.570 8.217
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.12-bioc/meat/signatureSearch.Rcheck/00check.log’
for details.
signatureSearch.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL signatureSearch
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘signatureSearch’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fastGSEA.cpp -o fastGSEA.o
In file included from fastGSEA.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fgsea_init.c -o fgsea_init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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 signatureSearch.so RcppExports.o fastGSEA.o fgsea_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-signatureSearch/00new/signatureSearch/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (signatureSearch)
signatureSearch.Rcheck/tests/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
0.254 0.062 0.296
signatureSearch.Rcheck/signatureSearch-Ex.timings
| name | user | system | elapsed | |
| add_pcid | 0.003 | 0.003 | 0.006 | |
| append2H5 | 0.071 | 0.006 | 0.078 | |
| build_custom_db | 0.360 | 0.042 | 0.405 | |
| cellNtestPlot | 1.778 | 0.138 | 2.175 | |
| cell_info | 0.112 | 0.007 | 0.119 | |
| chembl_moa_list | 0.004 | 0.002 | 0.006 | |
| clue_moa_list | 0.005 | 0.002 | 0.006 | |
| comp_fea_res | 0.186 | 0.003 | 0.189 | |
| create_empty_h5 | 0.028 | 0.003 | 0.032 | |
| dim-methods | 0.010 | 0.001 | 0.011 | |
| drug_cell_ranks | 0.008 | 0.001 | 0.009 | |
| drugs-methods | 0.002 | 0.000 | 0.003 | |
| drugs10 | 0.002 | 0.001 | 0.003 | |
| dsea_GSEA | 0.002 | 0.001 | 0.004 | |
| dsea_hyperG | 0.001 | 0.001 | 0.003 | |
| dtnetplot | 7.224 | 0.570 | 8.217 | |
| enrichGO2 | 0.001 | 0.000 | 0.000 | |
| enrichKEGG2 | 0.001 | 0.000 | 0.000 | |
| enrichMOA | 0.048 | 0.004 | 0.053 | |
| enrichReactome | 0.001 | 0.001 | 0.000 | |
| feaResult | 0.002 | 0.001 | 0.003 | |
| gctx2h5 | 0.979 | 0.269 | 1.310 | |
| gessResult | 0.002 | 0.000 | 0.003 | |
| gess_cmap | 0.001 | 0.001 | 0.002 | |
| gess_cor | 0.000 | 0.001 | 0.001 | |
| gess_fisher | 0.002 | 0.001 | 0.002 | |
| gess_gcmap | 0.001 | 0.000 | 0.002 | |
| gess_lincs | 0.001 | 0.000 | 0.001 | |
| gess_res_vis | 0.305 | 0.003 | 0.310 | |
| getSig | 3.299 | 0.097 | 3.780 | |
| get_targets | 4.100 | 0.063 | 4.504 | |
| get_treat_info | 1.377 | 0.029 | 1.598 | |
| gmt2h5 | 0.125 | 0.019 | 0.144 | |
| gseGO2 | 0.001 | 0.002 | 0.003 | |
| gseKEGG2 | 0.010 | 0.001 | 0.011 | |
| gseReactome | 0.009 | 0.001 | 0.010 | |
| head-methods | 0.006 | 0.001 | 0.007 | |
| lincs_expr_inst_info | 0.040 | 0.003 | 0.043 | |
| lincs_pert_info | 0.064 | 0.004 | 0.069 | |
| lincs_sig_info | 0.041 | 0.003 | 0.044 | |
| mabsGO | 0.002 | 0.001 | 0.003 | |
| mabsKEGG | 0.01 | 0.00 | 0.01 | |
| mabsReactome | 0.01 | 0.00 | 0.01 | |
| matrix2h5 | 0.068 | 0.005 | 0.074 | |
| moa_conn | 0.031 | 0.003 | 0.035 | |
| parse_gctx | 0.107 | 0.006 | 0.113 | |
| qSig | 3.160 | 0.103 | 3.720 | |
| rand_query_ES | 3.449 | 0.340 | 3.802 | |
| read_gmt | 0.001 | 0.000 | 0.000 | |
| result-methods | 0.033 | 0.001 | 0.033 | |
| runWF | 60.027 | 1.364 | 69.526 | |
| set_readable | 31.869 | 1.182 | 33.540 | |
| show-methods | 0.048 | 0.001 | 0.049 | |
| sim_score_grp | 0.019 | 0.000 | 0.019 | |
| tail-methods | 0.008 | 0.000 | 0.008 | |
| tarReduce | 0.001 | 0.000 | 0.001 | |
| targetList | 0.003 | 0.002 | 0.005 | |
| tsea_dup_hyperG | 0.001 | 0.002 | 0.004 | |
| tsea_mGSEA | 0.001 | 0.002 | 0.003 | |
| tsea_mabs | 0.001 | 0.002 | 0.003 | |
| vec_char_redu | 0.000 | 0.001 | 0.000 | |