| Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-05-29 11:07:24 -0400 (Mon, 29 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.0 RC (2023-04-13 r84269) -- "Already Tomorrow" | 4617 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.0 RC (2023-04-13 r84269 ucrt) -- "Already Tomorrow" | 4368 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.0 RC (2023-04-13 r84257) -- "Already Tomorrow" | 4326 |
| 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 1913/2229 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| signatureSearch 1.14.0 (landing page) Brendan Gongol
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: signatureSearch |
| Version: 1.14.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings signatureSearch_1.14.0.tar.gz |
| StartedAt: 2023-05-29 07:19:40 -0400 (Mon, 29 May 2023) |
| EndedAt: 2023-05-29 07:38:00 -0400 (Mon, 29 May 2023) |
| EllapsedTime: 1100.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: signatureSearch.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings signatureSearch_1.14.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/signatureSearch.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84257)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘signatureSearch/DESCRIPTION’ ... OK
* this is package ‘signatureSearch’ version ‘1.14.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 87.6Mb
sub-directories of 1Mb or more:
R 82.8Mb
data 2.9Mb
extdata 1.5Mb
* 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 ... 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 102.400 3.920 136.665
runWF 46.338 3.302 71.983
rand_query_ES 11.470 4.120 19.042
addGESSannot 7.425 1.496 17.668
dtnetplot 4.447 0.310 6.201
* 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: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc/meat/signatureSearch.Rcheck/00check.log’
for details.
signatureSearch.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL signatureSearch ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘signatureSearch’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastGSEA.cpp -o fastGSEA.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fgsea_init.c -o fgsea_init.o clang++ -arch x86_64 -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/opt/R/x86_64/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/4.3-x86_64/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 4.3.0 RC (2023-04-13 r84257) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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
0.359 0.114 0.467
signatureSearch.Rcheck/signatureSearch-Ex.timings
| name | user | system | elapsed | |
| addGESSannot | 7.425 | 1.496 | 17.668 | |
| addMOA | 0.546 | 0.009 | 0.701 | |
| add_pcid | 0.002 | 0.004 | 0.010 | |
| append2H5 | 0.147 | 0.019 | 0.227 | |
| build_custom_db | 0.565 | 0.080 | 0.851 | |
| cellNtestPlot | 1.332 | 0.125 | 1.958 | |
| cell_info | 0.042 | 0.005 | 0.056 | |
| cell_info2 | 0.067 | 0.004 | 0.091 | |
| chembl_moa_list | 0.005 | 0.005 | 0.014 | |
| clue_moa_list | 0.005 | 0.004 | 0.013 | |
| comp_fea_res | 0.381 | 0.004 | 0.476 | |
| create_empty_h5 | 0.042 | 0.004 | 0.059 | |
| dim-methods | 0.014 | 0.001 | 0.019 | |
| drug_cell_ranks | 0.016 | 0.000 | 0.020 | |
| drugs-methods | 0.004 | 0.001 | 0.007 | |
| drugs10 | 0.002 | 0.004 | 0.010 | |
| dtnetplot | 4.447 | 0.310 | 6.201 | |
| enrichGO2 | 0.000 | 0.000 | 0.001 | |
| enrichKEGG2 | 0.001 | 0.000 | 0.001 | |
| enrichMOA | 0.065 | 0.008 | 0.090 | |
| enrichReactome | 0.000 | 0.001 | 0.001 | |
| fea | 0.004 | 0.006 | 0.010 | |
| feaResult | 0.004 | 0.000 | 0.004 | |
| gctx2h5 | 1.085 | 0.496 | 2.024 | |
| gess | 0.002 | 0.002 | 0.003 | |
| gessResult | 0.003 | 0.001 | 0.007 | |
| gess_res_vis | 0.616 | 0.008 | 0.831 | |
| getSig | 2.305 | 0.291 | 3.878 | |
| getTreats | 0.801 | 0.091 | 1.323 | |
| get_targets | 3.340 | 0.205 | 4.769 | |
| gmt2h5 | 0.195 | 0.039 | 0.301 | |
| gseGO2 | 0.002 | 0.004 | 0.005 | |
| gseKEGG2 | 0.016 | 0.001 | 0.022 | |
| gseReactome | 0.016 | 0.002 | 0.026 | |
| head-methods | 0.012 | 0.002 | 0.017 | |
| lincs_expr_inst_info | 0.063 | 0.005 | 0.087 | |
| lincs_pert_info | 0.180 | 0.008 | 0.236 | |
| lincs_pert_info2 | 0.618 | 0.042 | 0.850 | |
| lincs_sig_info | 0.078 | 0.006 | 0.109 | |
| list2df | 0.004 | 0.000 | 0.006 | |
| list_rev | 0.003 | 0.001 | 0.004 | |
| mabsGO | 0.002 | 0.004 | 0.007 | |
| mabsKEGG | 0.018 | 0.002 | 0.026 | |
| mabsReactome | 0.018 | 0.002 | 0.025 | |
| matrix2h5 | 0.116 | 0.011 | 0.162 | |
| meanExpr2h5 | 1.071 | 0.416 | 1.878 | |
| moa_conn | 0.053 | 0.005 | 0.078 | |
| parse_gctx | 1.288 | 0.035 | 1.711 | |
| qSig | 1.636 | 0.220 | 2.728 | |
| rand_query_ES | 11.470 | 4.120 | 19.042 | |
| read_gmt | 0.005 | 0.003 | 0.007 | |
| result-methods | 0.064 | 0.015 | 0.079 | |
| runWF | 46.338 | 3.302 | 71.983 | |
| set_readable | 102.400 | 3.920 | 136.665 | |
| show-methods | 0.063 | 0.003 | 0.091 | |
| sim_score_grp | 0.020 | 0.001 | 0.028 | |
| tail-methods | 0.013 | 0.002 | 0.019 | |
| tarReduce | 0.001 | 0.000 | 0.001 | |
| targetList | 0.005 | 0.004 | 0.012 | |
| vec_char_redu | 0.000 | 0.000 | 0.003 | |