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This page was generated on 2024-06-14 14:38 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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

Package 788/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRcore 1.2.0  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/gDRcore
git_branch: RELEASE_3_19
git_last_commit: 8b5ff22
git_last_commit_date: 2024-04-30 11:50:21 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for gDRcore on palomino3

To the developers/maintainers of the gDRcore package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gDRcore.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: gDRcore
Version: 1.2.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gDRcore.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings gDRcore_1.2.0.tar.gz
StartedAt: 2024-06-13 03:59:14 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 04:07:13 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 479.3 seconds
RetCode: 0
Status:   OK  
CheckDir: gDRcore.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gDRcore.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings gDRcore_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/gDRcore.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'gDRcore/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gDRcore' version '1.2.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'gDRcore' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* 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 code 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 whether startup messages can be suppressed ... 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 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-3.19-bioc/R/library/gDRcore/libs/x64/gDRcore.dll':
  Found '_exit', possibly from '_exit' (C)
  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
runDrugResponseProcessingPipelineFxns 19.22   2.08   21.89
add_CellLine_annotation                5.34   2.37   28.99
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'F:/biocbuild/bbs-3.19-bioc/meat/gDRcore.Rcheck/00check.log'
for details.


Installation output

gDRcore.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL gDRcore
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'gDRcore' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c gDRcore.cpp -o gDRcore.o
g++ -std=gnu++17 -shared -s -static-libgcc -o gDRcore.dll tmp.def gDRcore.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-gDRcore/00new/gDRcore/libs/x64
** R
** 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 (gDRcore)

Tests output

gDRcore.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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("gDRcore")
> library("testthat")
> 
> test_check("gDRcore")
INFO [2024-06-13 04:02:44] Merge with Cell line info
INFO [2024-06-13 04:02:44] Merge with Cell line info
INFO [2024-06-13 04:06:26] 
INFO [2024-06-13 04:06:44] Manifest loaded successfully
INFO [2024-06-13 04:06:44] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2024-06-13 04:06:44] Loading Template_7daytreated.xlsx
INFO [2024-06-13 04:06:44] Loading Template_Untreated.xlsx
INFO [2024-06-13 04:06:45] Templates loaded successfully!
INFO [2024-06-13 04:06:45] Reading file F:/biocbuild/bbs-3.19-bioc/R/library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-06-13 04:06:45] Plate 201904190a read; 384 wells
INFO [2024-06-13 04:06:45] Plate 201904190b read; 384 wells
INFO [2024-06-13 04:06:45] Plate 201904190c read; 384 wells
INFO [2024-06-13 04:06:45] Plate 201904190d read; 384 wells
INFO [2024-06-13 04:06:45] Plate 201904190e read; 384 wells
INFO [2024-06-13 04:06:45] Plate 201904190f read; 384 wells
INFO [2024-06-13 04:06:45] File done
INFO [2024-06-13 04:06:45] Reading file F:/biocbuild/bbs-3.19-bioc/R/library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-06-13 04:06:46] Plate 201904197a read; 384 wells
INFO [2024-06-13 04:06:46] Plate 201904197b read; 384 wells
INFO [2024-06-13 04:06:46] Plate 201904197c read; 384 wells
INFO [2024-06-13 04:06:46] Plate 201904197d read; 384 wells
INFO [2024-06-13 04:06:46] Plate 201904197e read; 384 wells
INFO [2024-06-13 04:06:46] Plate 201904197f read; 384 wells
INFO [2024-06-13 04:06:46] File done
INFO [2024-06-13 04:06:46] Manifest loaded successfully
INFO [2024-06-13 04:06:46] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2024-06-13 04:06:46] Loading Template_7daytreated.xlsx
INFO [2024-06-13 04:06:46] Loading Template_Untreated.xlsx
INFO [2024-06-13 04:06:47] Templates loaded successfully!
INFO [2024-06-13 04:06:47] Reading file F:/biocbuild/bbs-3.19-bioc/R/library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-06-13 04:06:47] Plate 201904190a read; 384 wells
INFO [2024-06-13 04:06:47] Plate 201904190b read; 384 wells
INFO [2024-06-13 04:06:47] Plate 201904190c read; 384 wells
INFO [2024-06-13 04:06:47] Plate 201904190d read; 384 wells
INFO [2024-06-13 04:06:47] Plate 201904190e read; 384 wells
INFO [2024-06-13 04:06:47] Plate 201904190f read; 384 wells
INFO [2024-06-13 04:06:47] File done
INFO [2024-06-13 04:06:47] Reading file F:/biocbuild/bbs-3.19-bioc/R/library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-06-13 04:06:47] Plate 201904197a read; 384 wells
INFO [2024-06-13 04:06:47] Plate 201904197b read; 384 wells
INFO [2024-06-13 04:06:47] Plate 201904197c read; 384 wells
INFO [2024-06-13 04:06:47] Plate 201904197d read; 384 wells
INFO [2024-06-13 04:06:47] Plate 201904197e read; 384 wells
INFO [2024-06-13 04:06:47] Plate 201904197f read; 384 wells
INFO [2024-06-13 04:06:47] File done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 197 ]
> 
> proc.time()
   user  system elapsed 
 245.82   18.18  265.45 

Example timings

gDRcore.Rcheck/gDRcore-Ex.timings

nameusersystemelapsed
add_CellLine_annotation 5.34 2.3728.99
add_Drug_annotation0.970.781.79
calculate_GR_value000
calculate_excess0.080.000.08
calculate_matrix_metric0.010.020.03
cleanup_metadata0.190.280.48
convert_mae_to_raw_data1.030.811.97
convert_se_to_raw_data0.660.020.67
data_model000
dot-standardize_conc0.010.000.02
fit_SE.combinations3.390.283.75
get_default_nested_identifiers000
grr_matches0.020.000.01
identify_data_type0.030.000.03
identify_keys0.110.000.11
map_conc_to_standardized_conc0.010.000.01
map_df0.140.000.14
map_ids_to_fits000
merge_data1.720.932.97
prepare_input1.630.342.11
remove_drug_batch000
replace_conc_with_standardized_conc000
round_concentration000
runDrugResponseProcessingPipelineFxns19.22 2.0821.89
split_raw_data0.230.030.28
test_synthetic_data0.780.060.86