nebbiolo2 Summary
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| Package: HiTIMED |
| Version: 0.99.1 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data HiTIMED |
| BuildTime: 1 minutes 5.53 seconds |
| CheckCommand: BiocCheckGitClone('HiTIMED') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3030/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3030/1a62cf4f730cb80924d86371f17b81f7acc8391a/HiTIMED.install-out.txt HiTIMED_0.99.1.tar.gz && BiocCheck('HiTIMED_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 5 minutes 13.55 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 15.93 KiB |
| BuildID:: HiTIMED_20230530174138 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: HiTIMED. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. |
nebbiolo2 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘HiTIMED/DESCRIPTION’ ... OK
* preparing ‘HiTIMED’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘HiTIMED_0.99.1.tar.gz’
nebbiolo2 CHECK output
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===============================
BiocCheckGitClone('HiTIMED')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: HiTIMED
─ PackageVersion: 0.99.1
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3030/1a62cf4f730cb80924d86371f17b81f7acc8391a/HiTIMED
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* 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...
* Checking that provided CITATION file is correctly formatted...
* NOTE: CITATION file might be not correctly formatted
─ 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/3030/1a62cf4f730cb80924d86371f17b81f7acc8391a/HiTIMED.Rcheck’
* using R version 4.3.0 RC (2023-04-18 r84287)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiTIMED/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiTIMED’ version ‘0.99.1’
* 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 serialization versions ... OK
* checking whether package ‘HiTIMED’ can be installed ... OK
* 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
Error in c(bibentry(bibtype = "Article", key = "HiTIMED", title = "HiTIMED: hierarchical tumor immune microenvironment epigenetic deconvolution for accurate cell type resolution in the tumor microenvironment using tumor-type-specific DNA methylation data", author = c(person(given = "Ze", family = "Zhang"), person(given = "John", family = "Wiencke"), person(given = "Karl", family = "Kelsey"), person(given = "Brock", family = "Christensen"), person(given = "Lucas", family = "Salas")), year = "2022", month = "Nov", journal = "Journal of Translational Medicine", volume = "20", number = "516", doi = "10.1186/s12967-022-03736-6", pubmed = "36348337", language = "eng", header = "HiTIMED pipeline is described in:"), ): argument 2 is empty
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [13s/13s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/13s] OK
* checking loading without being on the library search path ... [13s/13s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘InfiniumPurify:::.get_peak’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [42s/42s] NOTE
HiTIMED_deconvolution: no visible global function definition for
‘query’
HiTIMED_deconvolution: no visible binding for global variable ‘Sum’
Undefined global functions or variables:
Sum query
* 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 files in ‘vignettes’ ... OK
* checking examples ... [21s/22s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
HiTIMED_deconvolution 5.234 0.64 6.899
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [22s/23s]
[22s/23s] 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 ... [2s/2s] OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3030/1a62cf4f730cb80924d86371f17b81f7acc8391a/HiTIMED.Rcheck/00check.log’
for details.
===============================
BiocCheck('HiTIMED_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: HiTIMED
─ PackageVersion: 0.99.1
─ sourceDir: /tmp/RtmpC774xM/file1affbc6bad6fab/HiTIMED
─ installDir: /tmp/RtmpC774xM/file1affbc1a1c3
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3030/1a62cf4f730cb80924d86371f17b81f7acc8391a/HiTIMED.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...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
ExperimentData
* 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...
* NOTE: The Description field in the DESCRIPTION is made up by less
than 3 sentences. Please consider expanding this field, and
structure it as a full paragraph
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* 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 HiTIMED...
* Checking coding practice...
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
is 1 function greater than 50 lines.
* Checking man page documentation...
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
* 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; 3 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 231 lines
(38%) 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 HiTIMED.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
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lconway Summary
[top]
| Package: HiTIMED |
| Version: 0.99.1 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data HiTIMED |
| BuildTime: 0 minutes 54.62 seconds |
| CheckCommand: BiocCheckGitClone('HiTIMED') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3030/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3030/1a62cf4f730cb80924d86371f17b81f7acc8391a/HiTIMED.install-out.txt HiTIMED_0.99.1.tar.gz && BiocCheck('HiTIMED_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 3 minutes 56.19 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh HiTIMED_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 30.70 seconds |
| PackageFileSize: 15.58 KiB |
| BuildID:: HiTIMED_20230530174138 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: HiTIMED. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. Build Package status: 0. |
lconway BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘HiTIMED/DESCRIPTION’ ... OK
* preparing ‘HiTIMED’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘HiTIMED_0.99.1.tar.gz’
lconway CHECK output
[top]
===============================
BiocCheckGitClone('HiTIMED')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: HiTIMED
─ PackageVersion: 0.99.1
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3030/1a62cf4f730cb80924d86371f17b81f7acc8391a/HiTIMED
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* 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...
* Checking that provided CITATION file is correctly formatted...
* NOTE: CITATION file might be not correctly formatted
─ 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/3030/1a62cf4f730cb80924d86371f17b81f7acc8391a/HiTIMED.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84266)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiTIMED/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiTIMED’ version ‘0.99.1’
* 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 serialization versions ... OK
* checking whether package ‘HiTIMED’ can be installed ... OK
* 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
Error in c(bibentry(bibtype = "Article", key = "HiTIMED", title = "HiTIMED: hierarchical tumor immune microenvironment epigenetic deconvolution for accurate cell type resolution in the tumor microenvironment using tumor-type-specific DNA methylation data", author = c(person(given = "Ze", family = "Zhang"), person(given = "John", family = "Wiencke"), person(given = "Karl", family = "Kelsey"), person(given = "Brock", family = "Christensen"), person(given = "Lucas", family = "Salas")), year = "2022", month = "Nov", journal = "Journal of Translational Medicine", volume = "20", number = "516", doi = "10.1186/s12967-022-03736-6", pubmed = "36348337", language = "eng", header = "HiTIMED pipeline is described in:"), ): argument 2 is empty
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘InfiniumPurify:::.get_peak’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [31s/31s] NOTE
HiTIMED_deconvolution: no visible global function definition for
‘query’
HiTIMED_deconvolution: no visible binding for global variable ‘Sum’
Undefined global functions or variables:
Sum query
* 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 files in ‘vignettes’ ... OK
* checking examples ... [16s/17s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
HiTIMED_deconvolution 4.304 0.616 5.922
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [16s/18s]
[17s/18s] 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 ... [3s/4s] OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3030/1a62cf4f730cb80924d86371f17b81f7acc8391a/HiTIMED.Rcheck/00check.log’
for details.
===============================
BiocCheck('HiTIMED_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: HiTIMED
─ PackageVersion: 0.99.1
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp8NOQz0/file1169eac7448f/HiTIMED
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp8NOQz0/file1169ec14e34e
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3030/1a62cf4f730cb80924d86371f17b81f7acc8391a/HiTIMED.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...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
ExperimentData
* 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...
* NOTE: The Description field in the DESCRIPTION is made up by less
than 3 sentences. Please consider expanding this field, and
structure it as a full paragraph
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* 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 HiTIMED...
* Checking coding practice...
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
is 1 function greater than 50 lines.
* Checking man page documentation...
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
* 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; 3 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 231 lines
(38%) 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 HiTIMED.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
lconway BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir HiTIMED_0.99.1.tar.gz'
>>>>>>>
* installing *source* package ‘HiTIMED’ ...
** using staged installation
** 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 (HiTIMED)