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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 772/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRcore 1.5.3  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/gDRcore
git_branch: devel
git_last_commit: a08b10a
git_last_commit_date: 2024-12-18 10:52:50 -0500 (Wed, 18 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for gDRcore on nebbiolo1

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: 1.5.3
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:gDRcore.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings gDRcore_1.5.3.tar.gz
StartedAt: 2024-12-23 22:12:49 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 22:18:32 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 342.6 seconds
RetCode: 0
Status:   OK  
CheckDir: gDRcore.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:gDRcore.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings gDRcore_1.5.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/gDRcore.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘gDRcore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRcore’ version ‘1.5.3’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘gDRcore’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 loading without being on the library search path ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fit_SE.combinations.Rd: SummarizedExperiment-class
  runDrugResponseProcessingPipelineFxns.Rd: SummarizedExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 is not available
File ‘gDRcore/libs/gDRcore.so’:
  Found non-API call to R: ‘STRING_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                        user system elapsed
runDrugResponseProcessingPipelineFxns 16.785  0.348  16.679
annotate_dt_with_cell_line             5.100  0.203   5.305
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/gDRcore.Rcheck/00check.log’
for details.


Installation output

gDRcore.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL gDRcore
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘gDRcore’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c gDRcore.cpp -o gDRcore.o
gDRcore.cpp:6: warning: "R_NO_REMAP" redefined
    6 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o gDRcore.so gDRcore.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-gDRcore/00new/gDRcore/libs
** 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
** 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 (gDRcore)

Tests output

gDRcore.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 [2024-12-23 22:17:32] 
INFO [2024-12-23 22:17:32] 
INFO [2024-12-23 22:17:32] 
INFO [2024-12-23 22:17:49] Manifest loaded successfully
INFO [2024-12-23 22:17:49] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2024-12-23 22:17:49] Loading Template_7daytreated.xlsx
INFO [2024-12-23 22:17:49] Loading Template_Untreated.xlsx
INFO [2024-12-23 22:17:49] Templates loaded successfully!
INFO [2024-12-23 22:17:49] Reading file /home/biocbuild/bbs-3.21-bioc/R/site-library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-12-23 22:17:50] Plate 201904190a read; 384 wells
INFO [2024-12-23 22:17:50] Plate 201904190b read; 384 wells
INFO [2024-12-23 22:17:50] Plate 201904190c read; 384 wells
INFO [2024-12-23 22:17:50] Plate 201904190d read; 384 wells
INFO [2024-12-23 22:17:50] Plate 201904190e read; 384 wells
INFO [2024-12-23 22:17:50] Plate 201904190f read; 384 wells
INFO [2024-12-23 22:17:50] File done
INFO [2024-12-23 22:17:50] Reading file /home/biocbuild/bbs-3.21-bioc/R/site-library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-12-23 22:17:50] Plate 201904197a read; 384 wells
INFO [2024-12-23 22:17:50] Plate 201904197b read; 384 wells
INFO [2024-12-23 22:17:50] Plate 201904197c read; 384 wells
INFO [2024-12-23 22:17:50] Plate 201904197d read; 384 wells
INFO [2024-12-23 22:17:50] Plate 201904197e read; 384 wells
INFO [2024-12-23 22:17:50] Plate 201904197f read; 384 wells
INFO [2024-12-23 22:17:50] File done
INFO [2024-12-23 22:17:50] Manifest loaded successfully
INFO [2024-12-23 22:17:50] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2024-12-23 22:17:50] Loading Template_7daytreated.xlsx
INFO [2024-12-23 22:17:50] Loading Template_Untreated.xlsx
INFO [2024-12-23 22:17:50] Templates loaded successfully!
INFO [2024-12-23 22:17:50] Reading file /home/biocbuild/bbs-3.21-bioc/R/site-library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-12-23 22:17:51] Plate 201904190a read; 384 wells
INFO [2024-12-23 22:17:51] Plate 201904190b read; 384 wells
INFO [2024-12-23 22:17:51] Plate 201904190c read; 384 wells
INFO [2024-12-23 22:17:51] Plate 201904190d read; 384 wells
INFO [2024-12-23 22:17:51] Plate 201904190e read; 384 wells
INFO [2024-12-23 22:17:51] Plate 201904190f read; 384 wells
INFO [2024-12-23 22:17:51] File done
INFO [2024-12-23 22:17:51] Reading file /home/biocbuild/bbs-3.21-bioc/R/site-library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-12-23 22:17:51] Plate 201904197a read; 384 wells
INFO [2024-12-23 22:17:51] Plate 201904197b read; 384 wells
INFO [2024-12-23 22:17:51] Plate 201904197c read; 384 wells
INFO [2024-12-23 22:17:51] Plate 201904197d read; 384 wells
INFO [2024-12-23 22:17:51] Plate 201904197e read; 384 wells
INFO [2024-12-23 22:17:51] Plate 201904197f read; 384 wells
INFO [2024-12-23 22:17:51] File done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 226 ]
> 
> proc.time()
   user  system elapsed 
218.173   2.174 219.285 

Example timings

gDRcore.Rcheck/gDRcore-Ex.timings

nameusersystemelapsed
annotate_dt_with_cell_line5.1000.2035.305
annotate_dt_with_drug0.0140.0010.015
calculate_GR_value0.0020.0020.002
calculate_excess0.0610.0090.071
calculate_matrix_metric0.0160.0080.024
calculate_score0.0330.0050.040
cleanup_metadata0.2660.0190.285
convert_mae_to_raw_data1.5310.0651.566
convert_se_to_raw_data0.1060.0010.087
data_model0.0030.0000.001
dot-standardize_conc0.0020.0000.002
fit_SE.combinations2.7680.0972.857
get_cell_line_annotation0.0040.0020.006
get_cellline_annotation_from_dt0.0070.0010.008
get_default_nested_identifiers0.0000.0010.001
get_drug_annotation0.0040.0020.005
get_drug_annotation_from_dt0.0050.0000.005
grr_matches0.0140.0000.014
identify_data_type0.040.000.04
identify_keys0.0990.0030.102
map_conc_to_standardized_conc0.0030.0000.004
map_df0.1080.0020.110
map_ids_to_fits0.0010.0000.002
merge_data1.4260.1081.466
prepare_input1.3010.0621.282
process_perturbations0.0060.0000.006
remove_drug_batch0.0000.0010.000
replace_conc_with_standardized_conc0.0010.0000.001
runDrugResponseProcessingPipelineFxns16.785 0.34816.679
split_raw_data0.3620.0280.322
test_synthetic_data0.9720.0180.954