lconway Summary
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| Package: smoppix |
| Version: 0.99.13 |
| RVersion: 4.4
|
| BiocVersion: 3.20
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data smoppix |
| BuildTime: 5 minutes 9.55 seconds |
| CheckCommand: BiocCheckGitClone('smoppix') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3379/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3379/8bfa96ce57ab0944dd051618e7dc35894fd084e8/smoppix.install-out.txt smoppix_0.99.13.tar.gz && BiocCheck('smoppix_0.99.13.tar.gz', `new-package`=TRUE) |
| CheckTime: 6 minutes 24.81 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh smoppix_0.99.13.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 23.89 seconds |
| PackageFileSize: 4659.77 KiB |
| BuildID:: smoppix_20240722154938 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: smoppix. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0. Build Package status: 0. |
lconway BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘smoppix/DESCRIPTION’ ... OK
* preparing ‘smoppix’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
Loading required namespace: smoppix
* saving partial Rd database
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘smoppix_0.99.13.tar.gz’
lconway CHECK output
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===============================
BiocCheckGitClone('smoppix')
===============================
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3379/8bfa96ce57ab0944dd051618e7dc35894fd084e8/smoppix
─ BiocVersion: 3.20
─ Package: smoppix
─ PackageVersion: 0.99.13
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3379/8bfa96ce57ab0944dd051618e7dc35894fd084e8/smoppix.BiocCheck
─ BiocCheckVersion: 1.41.6
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3379/8bfa96ce57ab0944dd051618e7dc35894fd084e8/smoppix
─ installDir: NULL
─ isTarBall: FALSE
─ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* NOTE: (Optional) CITATION file not found. Only include a CITATION
file if there is a preprint or publication for this Bioconductor
package. Note that Bioconductor packages are not required to have
a CITATION file but it is useful both for users and for tracking
Bioconductor project-wide metrics. When including a CITATION
file, add the publication using the 'doi' argument of
'bibentry()'.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3379/8bfa96ce57ab0944dd051618e7dc35894fd084e8/smoppix.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘smoppix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘smoppix’ version ‘0.99.13’
* 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 ‘smoppix’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the package can be unloaded cleanly ... [5s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] OK
* checking use of S3 registration ... 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 ... [19s/20s] NOTE
plotCells: no visible binding for global variable ‘gene’
plotCells: no visible binding for global variable ‘cell’
plotWf: no visible binding for global variable ‘minP’
plotWf: no visible binding for global variable ‘maxP’
plotWf: no visible binding for global variable ‘Weight’
Undefined global functions or variables:
Weight cell gene maxP minP
* checking Rd files ... [6s/6s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] NOTE
Note: found 4 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... 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
* checking files in ‘vignettes’ ... OK
* checking examples ... [98s/77s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
evalWeightFunction 6.845 1.668 6.950
plotTopResults 6.642 1.656 6.259
getResults 6.311 1.729 6.752
getPvaluesGradient 6.212 1.434 7.245
writeToXlsx 5.004 1.505 4.584
fitLMMs 4.876 1.587 4.442
estGradients 3.209 0.669 7.433
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [235s/172s]
[235s/173s] 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 ... [4s/5s] OK
* DONE
Status: 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3379/8bfa96ce57ab0944dd051618e7dc35894fd084e8/smoppix.Rcheck/00check.log’
for details.
===============================
BiocCheck('smoppix_0.99.13.tar.gz')
===============================
* Installing package...
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix
─ BiocVersion: 3.20
─ Package: smoppix
─ PackageVersion: 0.99.13
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3379/8bfa96ce57ab0944dd051618e7dc35894fd084e8/smoppix.BiocCheck
─ BiocCheckVersion: 1.41.6
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd436b99ae
─ isTarBall: TRUE
─ platform: unix
* 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...
* 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 proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (15%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* WARNING: Package listed as VignetteEngine or VignetteBuilder but
not currently Suggested.
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/calcWindowDistPI.Rd:26: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/calcWindowDistPI.Rd:31: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/Eng.Rd:27: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/Eng.Rd:33: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/Yang.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/Yang.Rd:28: unknown macro '\insertAllCited'
* Checking for library/require of smoppix...
* 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 15 functions greater than 50 lines.
* Checking man page documentation...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/calcWindowDistPI.Rd:26: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/calcWindowDistPI.Rd:31: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/Eng.Rd:27: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/Eng.Rd:33: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/Yang.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/Yang.Rd:28: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/calcWindowDistPI.Rd:26: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/calcWindowDistPI.Rd:31: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/Eng.Rd:27: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/Eng.Rd:33: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/Yang.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/Yang.Rd:28: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/calcWindowDistPI.Rd:26: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/calcWindowDistPI.Rd:31: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/Eng.Rd:27: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/Eng.Rd:33: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/Yang.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpQRQv6R/file9bd22e662f8/smoppix/man/Yang.Rd:28: unknown macro '\insertAllCited'
* 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; 344 lines (10%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 42 lines
(1%) 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 is in the Support Site Watched Tags.
─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 3 NOTES
See the smoppix.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
lconway BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir smoppix_0.99.13.tar.gz'
>>>>>>>
* installing *source* package ‘smoppix’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c crossdistFast.cpp -o crossdistFast.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c findRanksDist.cpp -o findRanksDist.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o smoppix.so RcppExports.o crossdistFast.o findRanksDist.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/pkgbuild/packagebuilder/workers/jobs/3379/8bfa96ce57ab0944dd051618e7dc35894fd084e8/libdir/00LOCK-smoppix/00new/smoppix/libs
** R
** data
** 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 (smoppix)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR libdir/smoppix/libs/smoppix.so
>>>>>>>
>>>>>>> Paths before fix:
libdir/smoppix/libs/smoppix.so:
smoppix.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "libdir/smoppix/libs/smoppix.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "libdir/smoppix/libs/smoppix.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "libdir/smoppix/libs/smoppix.so"
>>>>>>> Paths after fix:
libdir/smoppix/libs/smoppix.so:
smoppix.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
nebbiolo2 Summary
[top]
| Package: smoppix |
| Version: 0.99.13 |
| RVersion: 4.4
|
| BiocVersion: 3.20
|
| BuildCommand: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data smoppix |
| BuildTime: 8 minutes 2.88 seconds |
| CheckCommand: BiocCheckGitClone('smoppix') && /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3379/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3379/8bfa96ce57ab0944dd051618e7dc35894fd084e8/smoppix.install-out.txt smoppix_0.99.13.tar.gz && BiocCheck('smoppix_0.99.13.tar.gz', `new-package`=TRUE) |
| CheckTime: 8 minutes 53.15 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 4328.39 KiB |
| BuildID:: smoppix_20240722154938 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: smoppix. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0. |
nebbiolo2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘smoppix/DESCRIPTION’ ... OK
* preparing ‘smoppix’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
Loading required namespace: smoppix
* saving partial Rd database
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘smoppix_0.99.13.tar.gz’
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('smoppix')
===============================
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3379/8bfa96ce57ab0944dd051618e7dc35894fd084e8/smoppix
─ BiocVersion: 3.20
─ Package: smoppix
─ PackageVersion: 0.99.13
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3379/8bfa96ce57ab0944dd051618e7dc35894fd084e8/smoppix.BiocCheck
─ BiocCheckVersion: 1.41.6
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3379/8bfa96ce57ab0944dd051618e7dc35894fd084e8/smoppix
─ installDir: NULL
─ isTarBall: FALSE
─ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* NOTE: (Optional) CITATION file not found. Only include a CITATION
file if there is a preprint or publication for this Bioconductor
package. Note that Bioconductor packages are not required to have
a CITATION file but it is useful both for users and for tracking
Bioconductor project-wide metrics. When including a CITATION
file, add the publication using the 'doi' argument of
'bibentry()'.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3379/8bfa96ce57ab0944dd051618e7dc35894fd084e8/smoppix.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘smoppix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘smoppix’ version ‘0.99.13’
* 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 ‘smoppix’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] OK
* checking use of S3 registration ... 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 ... [27s/27s] NOTE
plotCells: no visible binding for global variable ‘gene’
plotCells: no visible binding for global variable ‘cell’
plotWf: no visible binding for global variable ‘minP’
plotWf: no visible binding for global variable ‘maxP’
plotWf: no visible binding for global variable ‘Weight’
Undefined global functions or variables:
Weight cell gene maxP minP
* checking Rd files ... [8s/8s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] NOTE
Note: found 4 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... 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
* checking files in ‘vignettes’ ... OK
* checking examples ... [133s/101s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
evalWeightFunction 11.139 2.608 10.466
getResults 9.944 2.606 10.038
plotTopResults 8.849 1.876 7.905
estGradients 8.960 1.383 10.218
writeToXlsx 6.601 1.861 5.641
fitLMMs 6.382 1.879 5.392
getPvaluesGradient 3.658 0.590 9.031
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [343s/252s]
[344s/252s] 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 ... [3s/3s] OK
* DONE
Status: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3379/8bfa96ce57ab0944dd051618e7dc35894fd084e8/smoppix.Rcheck/00check.log’
for details.
===============================
BiocCheck('smoppix_0.99.13.tar.gz')
===============================
* Installing package...
─ sourceDir: /tmp/RtmprGfYfB/file1ba774c9ca317/smoppix
─ BiocVersion: 3.20
─ Package: smoppix
─ PackageVersion: 0.99.13
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3379/8bfa96ce57ab0944dd051618e7dc35894fd084e8/smoppix.BiocCheck
─ BiocCheckVersion: 1.41.6
─ sourceDir: /tmp/RtmprGfYfB/file1ba774c9ca317/smoppix
─ installDir: /tmp/RtmprGfYfB/file1ba774776797ff
─ isTarBall: TRUE
─ platform: unix
* 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...
* 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 proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (15%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* WARNING: Package listed as VignetteEngine or VignetteBuilder but
not currently Suggested.
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/calcWindowDistPI.Rd:26: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/calcWindowDistPI.Rd:31: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/Eng.Rd:27: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/Eng.Rd:33: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/Yang.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/Yang.Rd:28: unknown macro '\insertAllCited'
* Checking for library/require of smoppix...
* 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 15 functions greater than 50 lines.
* Checking man page documentation...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/calcWindowDistPI.Rd:26: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/calcWindowDistPI.Rd:31: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/Eng.Rd:27: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/Eng.Rd:33: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/Yang.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/Yang.Rd:28: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/calcWindowDistPI.Rd:26: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/calcWindowDistPI.Rd:31: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/Eng.Rd:27: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/Eng.Rd:33: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/Yang.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/Yang.Rd:28: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/calcWindowDistPI.Rd:26: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/calcWindowDistPI.Rd:31: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/Eng.Rd:27: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/Eng.Rd:33: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/Yang.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
/tmp/RtmprGfYfB/file1ba774c9ca317/smoppix/man/Yang.Rd:28: unknown macro '\insertAllCited'
* 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; 344 lines (10%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 42 lines
(1%) 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 is in the Support Site Watched Tags.
─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 3 NOTES
See the smoppix.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
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