| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-05-27 11:06:16 -0400 (Sat, 27 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 | ERROR | |||||||||
| 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: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:signatureSearch.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings signatureSearch_1.14.0.tar.gz |
| StartedAt: 2023-05-27 06:51:47 -0400 (Sat, 27 May 2023) |
| EndedAt: 2023-05-27 07:00:22 -0400 (Sat, 27 May 2023) |
| EllapsedTime: 515.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: signatureSearch.Rcheck |
| Warnings: 0 |
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### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:signatureSearch.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings signatureSearch_1.14.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/signatureSearch.Rcheck'
* using R version 4.3.0 RC (2023-04-13 r84269 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 whether package 'signatureSearch' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 88.5Mb
sub-directories of 1Mb or more:
R 82.8Mb
data 2.9Mb
extdata 1.5Mb
libs 1.0Mb
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/signatureSearch/libs/x64/signatureSearch.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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 nor [v]sprintf. 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
set_readable 48.92 2.64 51.64
runWF 27.00 2.99 37.08
addGESSannot 5.98 2.49 38.00
rand_query_ES 6.67 0.20 7.13
* 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
'F:/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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### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL signatureSearch
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'signatureSearch' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++11
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fastGSEA.cpp -o fastGSEA.o
fastGSEA.cpp: In function 'Rcpp::NumericVector calcGseaStatBatchCpp(const Rcpp::NumericVector&, const Rcpp::List&, const Rcpp::IntegerVector&)':
fastGSEA.cpp:444:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
444 | for (int j = 0; j < S.size(); ++j) {
| ~~^~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fgsea_init.c -o fgsea_init.o
g++ -shared -s -static-libgcc -o signatureSearch.dll tmp.def RcppExports.o fastGSEA.o fgsea_init.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-signatureSearch/00new/signatureSearch/libs/x64
** 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
** 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 r84269 ucrt) -- "Already Tomorrow"
Copyright (C) 2023 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
0.14 0.06 0.17
signatureSearch.Rcheck/signatureSearch-Ex.timings
| name | user | system | elapsed | |
| addGESSannot | 5.98 | 2.49 | 38.00 | |
| addMOA | 0.2 | 0.0 | 0.2 | |
| add_pcid | 0.00 | 0.01 | 0.01 | |
| append2H5 | 0.13 | 0.02 | 0.19 | |
| build_custom_db | 0.31 | 0.04 | 0.39 | |
| cellNtestPlot | 0.72 | 0.13 | 1.16 | |
| cell_info | 0.05 | 0.00 | 0.05 | |
| cell_info2 | 0.03 | 0.01 | 0.04 | |
| chembl_moa_list | 0.00 | 0.02 | 0.02 | |
| clue_moa_list | 0.00 | 0.02 | 0.01 | |
| comp_fea_res | 0.19 | 0.01 | 0.21 | |
| create_empty_h5 | 0.03 | 0.00 | 0.03 | |
| dim-methods | 0 | 0 | 0 | |
| drug_cell_ranks | 0.00 | 0.02 | 0.01 | |
| drugs-methods | 0 | 0 | 0 | |
| drugs10 | 0.01 | 0.00 | 0.02 | |
| dtnetplot | 1.93 | 0.23 | 2.66 | |
| enrichGO2 | 0 | 0 | 0 | |
| enrichKEGG2 | 0 | 0 | 0 | |
| enrichMOA | 0.04 | 0.00 | 0.08 | |
| enrichReactome | 0 | 0 | 0 | |
| fea | 0.00 | 0.01 | 0.01 | |
| feaResult | 0 | 0 | 0 | |
| gctx2h5 | 0.49 | 0.17 | 1.05 | |
| gess | 0 | 0 | 0 | |
| gessResult | 0 | 0 | 0 | |
| gess_res_vis | 0.26 | 0.00 | 0.27 | |
| getSig | 1.31 | 0.25 | 1.62 | |
| getTreats | 0.58 | 0.11 | 0.72 | |
| get_targets | 2.42 | 0.30 | 2.77 | |
| gmt2h5 | 0.10 | 0.08 | 0.47 | |
| gseGO2 | 0 | 0 | 0 | |
| gseKEGG2 | 0.01 | 0.00 | 0.01 | |
| gseReactome | 0.02 | 0.00 | 0.02 | |
| head-methods | 0 | 0 | 0 | |
| lincs_expr_inst_info | 0.03 | 0.01 | 0.04 | |
| lincs_pert_info | 1.13 | 0.02 | 1.14 | |
| lincs_pert_info2 | 0.20 | 0.03 | 0.24 | |
| lincs_sig_info | 0.03 | 0.00 | 0.03 | |
| list2df | 0 | 0 | 0 | |
| list_rev | 0 | 0 | 0 | |
| mabsGO | 0 | 0 | 0 | |
| mabsKEGG | 0.02 | 0.00 | 0.01 | |
| mabsReactome | 0.01 | 0.00 | 0.02 | |
| matrix2h5 | 0.02 | 0.01 | 0.11 | |
| meanExpr2h5 | 0.43 | 0.17 | 0.98 | |
| moa_conn | 0.02 | 0.02 | 0.03 | |
| parse_gctx | 0.05 | 0.03 | 0.08 | |
| qSig | 1.06 | 0.22 | 1.31 | |
| rand_query_ES | 6.67 | 0.20 | 7.13 | |
| read_gmt | 0.02 | 0.00 | 0.01 | |
| result-methods | 0.01 | 0.00 | 0.02 | |
| runWF | 27.00 | 2.99 | 37.08 | |
| set_readable | 48.92 | 2.64 | 51.64 | |
| show-methods | 0.04 | 0.00 | 0.03 | |
| sim_score_grp | 0.01 | 0.00 | 0.01 | |
| tail-methods | 0 | 0 | 0 | |
| tarReduce | 0 | 0 | 0 | |
| targetList | 0.00 | 0.01 | 0.02 | |
| vec_char_redu | 0 | 0 | 0 | |