===============================
R CMD BUILD
===============================
* checking for file ‘gDRcore/DESCRIPTION’ ... OK
* preparing ‘gDRcore’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘gDRcore_0.99.26.tar.gz’
===============================
BiocCheckGitClone('gDRcore')
===============================
─ BiocCheckVersion: 1.37.4
─ BiocVersion: 3.18
─ Package: gDRcore
─ PackageVersion: 0.99.26
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3003/52f9edad98a1e509acbe36f2af3b790165cf6366/gDRcore
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be Git tracked.
gDR.Rproj
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3003/52f9edad98a1e509acbe36f2af3b790165cf6366/gDRcore.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDRcore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRcore’ version ‘0.99.26’
* 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:
.github
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 ‘gDRcore’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... NOTE
Problems with news in ‘NEWS.md’:
Cannot extract version info from the following section titles:
remove backward compatibility for old data model
fix bug with missing rownames in normalized assay
update logic for merging data.table objects
replace order with data.table::setorder
switch from merge to [[ for data.table objects
switch from aggregate to data.table
switch from zoo::rollmean to data.table::frollmean
replaced reshape2 functions by functions from data.table
fix managing of mixed types of raw data
fix bug with subsetting data for calculating isobologram
format the vignette with BiocStyle
fix related with data.table
rename excess to x to unify colnames in assay data
refactor normalization_types in combo-specific assays
Utilize gDRutils::apply_bumpy_function in fit_SE
fix bug with swapping untreated/vehicle values
Fix bug with data.table
Utilize gDRutils::apply_bumpy_function in average_SE
switch to OSI license
Fix bug with replacing vehicle to untreated values
Moved wrapper fuctions from gDRtestData
Update dependencies
Add fix for bioc-devel (correct sorting in merge test)
Fix namespacing issue in examples
Fix examples for normalize_SE
add logic for retrieving raw data from assay data
update maintainer
bugfix for the logic in 'cleanup_metadata'
Make the package Bioc-compatible
Improve performance of 'map_df' with refactored logic for exact matches
Refactor pipeline
Address co-treatment fit by using the matrix data type instead
Add support for splitting normalization types
Remove obsolete code
Update path to annotation data
Clean-up code
Refactor mapping function to properly handle drug3
Replace parallelize function with gDRutils::loop
Add assert for vehicle values in input data in runDrugResponseProcessingPipeline
Fix error-handling if conditions in average_SE
Fix invalid encapsulation in tests
Add missing namespacing
Add support for setting number of cores for BiocParallel based on the env variable
Remove global parameters for BiocParallel
Change the logic for using cores in BiocParallel
Update the logic for parallel computing
Update the logic for default nested_confounders in create_SE function
Refactor create_SE to support reverse single-agent data
Release
Update
Refactored
Fixed
Added
Improved
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking startup messages can be suppressed ... [1s/1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'loadNamespace' or 'requireNamespace' call not declared from: ‘gDRinternalData’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [8s/8s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘gDRcore/libs/gDRcore.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... [69s/49s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runDrugResponseProcessingPipelineFxns 22.054 8.627 17.469
prepare_input 3.655 2.601 2.785
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [571s/266s]
[571s/266s] 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 ... [4s/4s] OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3003/52f9edad98a1e509acbe36f2af3b790165cf6366/gDRcore.Rcheck/00check.log’
for details.
===============================
BiocCheck('gDRcore_0.99.26.tar.gz')
===============================
─ BiocCheckVersion: 1.37.4
─ BiocVersion: 3.18
─ Package: gDRcore
─ PackageVersion: 0.99.26
─ sourceDir: /tmp/RtmplDguB9/fileda20930c2442c/gDRcore
─ installDir: /tmp/RtmplDguB9/fileda209346ff00f
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3003/52f9edad98a1e509acbe36f2af3b790165cf6366/gDRcore.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.2 to 4.3.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of gDRcore...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 22 functions greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 133 lines (2%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 2626 lines
(35%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 5 NOTES
See the gDRcore.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.