| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:31 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the signatureSearch package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/signatureSearch.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1894/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| signatureSearch 1.13.0 (landing page) Brendan Gongol
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: signatureSearch |
| Version: 1.13.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings signatureSearch_1.13.0.tar.gz |
| StartedAt: 2023-04-11 23:35:06 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 23:50:24 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 918.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: signatureSearch.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings signatureSearch_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/signatureSearch.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘signatureSearch/DESCRIPTION’ ... OK
* this is package ‘signatureSearch’ version ‘1.13.0’
* 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
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 87.9Mb
sub-directories of 1Mb or more:
R 82.6Mb
data 2.9Mb
extdata 1.3Mb
* 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 loading without being on the library search path ... 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 ... NOTE
Note: found 147 marked UTF-8 strings
* checking LazyData ... 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
set_readable 69.105 1.148 70.585
runWF 31.677 2.618 49.648
rand_query_ES 9.946 3.221 13.576
* 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 ...
‘signatureSearch.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/signatureSearch.Rcheck/00check.log’
for details.
signatureSearch.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL signatureSearch
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘signatureSearch’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -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 of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
444 | for (int j = 0; j < S.size(); ++j) {
| ~~^~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c fgsea_init.c -o fgsea_init.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o signatureSearch.so RcppExports.o fastGSEA.o fgsea_init.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-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 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
0.162 0.049 0.200
signatureSearch.Rcheck/signatureSearch-Ex.timings
| name | user | system | elapsed | |
| addGESSannot | 3.659 | 0.396 | 4.556 | |
| addMOA | 0.180 | 0.041 | 0.221 | |
| add_pcid | 0.000 | 0.001 | 0.002 | |
| append2H5 | 0.071 | 0.002 | 0.073 | |
| build_custom_db | 0.288 | 0.032 | 0.320 | |
| cellNtestPlot | 0.734 | 0.096 | 1.035 | |
| cell_info | 0.020 | 0.004 | 0.024 | |
| cell_info2 | 0.035 | 0.000 | 0.036 | |
| chembl_moa_list | 0.002 | 0.003 | 0.005 | |
| clue_moa_list | 0.004 | 0.000 | 0.004 | |
| comp_fea_res | 0.180 | 0.012 | 0.192 | |
| create_empty_h5 | 0.018 | 0.004 | 0.023 | |
| dim-methods | 0.005 | 0.004 | 0.008 | |
| drug_cell_ranks | 0.007 | 0.003 | 0.011 | |
| drugs-methods | 0.002 | 0.000 | 0.002 | |
| drugs10 | 0.002 | 0.000 | 0.002 | |
| dtnetplot | 2.143 | 0.305 | 2.740 | |
| enrichGO2 | 0 | 0 | 0 | |
| enrichKEGG2 | 0.000 | 0.001 | 0.000 | |
| enrichMOA | 0.038 | 0.003 | 0.041 | |
| enrichReactome | 0 | 0 | 0 | |
| fea | 0.000 | 0.002 | 0.002 | |
| feaResult | 0.002 | 0.000 | 0.002 | |
| gctx2h5 | 0.370 | 0.071 | 0.443 | |
| gess | 0.000 | 0.002 | 0.002 | |
| gessResult | 0.001 | 0.002 | 0.002 | |
| gess_res_vis | 0.312 | 0.019 | 0.332 | |
| getSig | 1.720 | 0.185 | 2.319 | |
| getTreats | 0.688 | 0.064 | 0.953 | |
| get_targets | 2.314 | 0.191 | 2.803 | |
| gmt2h5 | 0.084 | 0.015 | 0.101 | |
| gseGO2 | 0.001 | 0.000 | 0.001 | |
| gseKEGG2 | 0.01 | 0.00 | 0.01 | |
| gseReactome | 0.01 | 0.00 | 0.01 | |
| head-methods | 0.008 | 0.000 | 0.008 | |
| lincs_expr_inst_info | 0.105 | 0.000 | 0.105 | |
| lincs_pert_info | 0.113 | 0.004 | 0.117 | |
| lincs_pert_info2 | 1.272 | 0.184 | 1.456 | |
| lincs_sig_info | 0.034 | 0.004 | 0.038 | |
| list2df | 0.002 | 0.000 | 0.002 | |
| list_rev | 0.001 | 0.000 | 0.002 | |
| mabsGO | 0.001 | 0.000 | 0.002 | |
| mabsKEGG | 0.007 | 0.004 | 0.011 | |
| mabsReactome | 0.01 | 0.00 | 0.01 | |
| matrix2h5 | 0.051 | 0.003 | 0.054 | |
| meanExpr2h5 | 0.477 | 0.040 | 0.517 | |
| moa_conn | 0.020 | 0.004 | 0.024 | |
| parse_gctx | 0.076 | 0.000 | 0.076 | |
| qSig | 1.387 | 0.160 | 1.966 | |
| rand_query_ES | 9.946 | 3.221 | 13.576 | |
| read_gmt | 0.001 | 0.004 | 0.005 | |
| result-methods | 0.604 | 0.258 | 0.063 | |
| runWF | 31.677 | 2.618 | 49.648 | |
| set_readable | 69.105 | 1.148 | 70.585 | |
| show-methods | 0.032 | 0.004 | 0.036 | |
| sim_score_grp | 0.011 | 0.000 | 0.012 | |
| tail-methods | 0.006 | 0.002 | 0.007 | |
| tarReduce | 0.000 | 0.001 | 0.000 | |
| targetList | 0.003 | 0.001 | 0.003 | |
| vec_char_redu | 0.001 | 0.000 | 0.000 | |