Brendan Gongol
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/signatureSearch |
| git_branch: master |
| git_last_commit: 47d9d6a |
| git_last_commit_date: 2022-01-31 23:59:41 -0400 (Mon, 31 Jan 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:42 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1799/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| signatureSearch 1.9.7 (landing page) Brendan Gongol
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: signatureSearch |
| Version: 1.9.7 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:signatureSearch.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings signatureSearch_1.9.7.tar.gz |
| StartedAt: 2022-03-17 20:17:18 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:23:43 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 384.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: signatureSearch.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:signatureSearch.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings signatureSearch_1.9.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/signatureSearch.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.9.7'
* 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 ... NOTE
installed size is 88.9Mb
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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runWF 24.05 3.60 37.88
set_readable 17.54 3.14 21.48
* 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: 4 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/signatureSearch.Rcheck/00check.log'
for details.
signatureSearch.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL signatureSearch
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'signatureSearch' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 long unsigned int'} [-Wsign-compare]
for (int j = 0; j < S.size(); ++j) {
~~^~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c fgsea_init.c -o fgsea_init.o
C:/rtools40/mingw64/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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-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
converting help for package 'signatureSearch'
finding HTML links ... done
GCT-object html
addGESSannot html
addMOA html
add_pcid html
append2H5 html
build_custom_db html
calcGseaStatBatchCpp html
cellNtestPlot html
cell_info html
cell_info2 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
dtnetplot html
enrichGO2 html
enrichKEGG2 html
enrichMOA html
enrichReactome html
fea html
feaResult-class html
feaResult html
gctx2h5 html
gess html
gessResult-class html
gessResult html
gess_res_vis html
getALLEG html
getDb html
getSig html
getTreats html
get_targets html
gmt2h5 html
gseGO2 html
gseKEGG2 html
gseReactome html
head-methods html
lincs_expr_inst_info html
lincs_pert_info html
lincs_pert_info2 html
lincs_sig_info html
list2df html
list_rev html
mabsGO html
mabsKEGG html
mabsReactome html
matrix2h5 html
meanExpr2h5 html
moa_conn html
parse_gctx html
qSig-class html
qSig html
rand_query_ES html
read_gmt html
result-methods html
runWF html
set_readable html
show-methods html
signatureSearch-package html
sim_score_grp html
tail-methods html
tarReduce html
targetList html
vec_char_redu 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
* DONE (signatureSearch)
Making 'packages.html' ... done
signatureSearch.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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 0.03 0.14
signatureSearch.Rcheck/signatureSearch-Ex.timings
| name | user | system | elapsed | |
| addGESSannot | 2.62 | 1.19 | 4.86 | |
| addMOA | 0.14 | 0.00 | 0.14 | |
| add_pcid | 0.00 | 0.01 | 0.01 | |
| append2H5 | 0.03 | 0.02 | 0.11 | |
| build_custom_db | 0.27 | 0.00 | 0.33 | |
| cellNtestPlot | 0.62 | 0.06 | 1.11 | |
| cell_info | 0.02 | 0.00 | 0.02 | |
| cell_info2 | 0.03 | 0.00 | 0.03 | |
| chembl_moa_list | 0 | 0 | 0 | |
| clue_moa_list | 0 | 0 | 0 | |
| comp_fea_res | 0.11 | 0.00 | 0.11 | |
| create_empty_h5 | 0.02 | 0.00 | 0.03 | |
| dim-methods | 0 | 0 | 0 | |
| drug_cell_ranks | 0 | 0 | 0 | |
| drugs-methods | 0.01 | 0.00 | 0.02 | |
| drugs10 | 0 | 0 | 0 | |
| dtnetplot | 1.56 | 0.28 | 2.45 | |
| enrichGO2 | 0 | 0 | 0 | |
| enrichKEGG2 | 0 | 0 | 0 | |
| enrichMOA | 0.02 | 0.01 | 0.03 | |
| enrichReactome | 0 | 0 | 0 | |
| fea | 0.00 | 0.02 | 0.02 | |
| feaResult | 0 | 0 | 0 | |
| gctx2h5 | 1.06 | 0.11 | 1.26 | |
| gess | 0 | 0 | 0 | |
| gessResult | 0 | 0 | 0 | |
| gess_res_vis | 0.25 | 0.00 | 0.25 | |
| getSig | 1.13 | 0.20 | 2.19 | |
| getTreats | 0.47 | 0.11 | 1.05 | |
| get_targets | 1.65 | 0.19 | 2.48 | |
| gmt2h5 | 0.08 | 0.02 | 0.44 | |
| gseGO2 | 0 | 0 | 0 | |
| gseKEGG2 | 0.02 | 0.00 | 0.02 | |
| gseReactome | 0.01 | 0.00 | 0.01 | |
| head-methods | 0 | 0 | 0 | |
| lincs_expr_inst_info | 0.03 | 0.01 | 0.05 | |
| lincs_pert_info | 0.11 | 0.00 | 0.11 | |
| lincs_pert_info2 | 1.03 | 0.05 | 1.08 | |
| 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 | 0.02 | |
| mabsReactome | 0 | 0 | 0 | |
| matrix2h5 | 0.04 | 0.03 | 0.09 | |
| meanExpr2h5 | 0.49 | 0.12 | 0.69 | |
| moa_conn | 0.03 | 0.00 | 0.03 | |
| parse_gctx | 0.05 | 0.00 | 0.05 | |
| qSig | 1.03 | 0.14 | 2.06 | |
| rand_query_ES | 2.79 | 0.61 | 3.41 | |
| read_gmt | 0 | 0 | 0 | |
| result-methods | 0.02 | 0.00 | 0.01 | |
| runWF | 24.05 | 3.60 | 37.88 | |
| set_readable | 17.54 | 3.14 | 21.48 | |
| show-methods | 0.02 | 0.00 | 0.02 | |
| sim_score_grp | 0.01 | 0.00 | 0.01 | |
| tail-methods | 0 | 0 | 0 | |
| tarReduce | 0 | 0 | 0 | |
| targetList | 0 | 0 | 0 | |
| vec_char_redu | 0 | 0 | 0 | |