nebbiolo1 Summary
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| Package: CytoTalk |
| Version: 0.99.9 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data CytoTalk |
| BuildTime: 0 minutes 5.67 seconds |
| CheckCommand: BiocCheckGitClone('CytoTalk') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings CytoTalk_0.99.9.tar.gz && BiocCheck('CytoTalk_0.99.9.tar.gz', `new-package`=TRUE) |
| CheckTime: 1 minutes 8.46 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 4680.63 KiB |
| BuildID:: CytoTalk_20220225191204 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: CytoTalk. 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. Checking Package status: 0. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘CytoTalk/DESCRIPTION’ ... OK
* preparing ‘CytoTalk’:
* 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
* building ‘CytoTalk_0.99.9.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('CytoTalk')
===============================
This is BiocCheckGitClone version 1.31.34. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2508/68e83f2ac1e607335234ec9ba4c0d79a5abc5260/CytoTalk.Rcheck’
* using R Under development (unstable) (2022-02-17 r81757)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CytoTalk/DESCRIPTION’ ... OK
* this is package ‘CytoTalk’ version ‘0.99.9’
* 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 ‘CytoTalk’ can be installed ... [3s/3s] 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 ... OK
* checking R 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 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 ... [2s/2s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [43s/43s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
doc_mutinfo 34.395 0.16 34.557
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [0s/0s]
[1s/1s] 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 ... OK
* DONE
Status: OK
===============================
BiocCheck('CytoTalk_0.99.9.tar.gz')
===============================
This is BiocCheck version 1.31.34. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2508/68e83f2ac1e607335234ec9ba4c0d79a5abc5260/CytoTalk_0.99.9.tar.gz" "/tmp/RtmpxDvnoA/file2c403667ee4e4/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 3.5.0 to 4.2.0.
* 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...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of CytoTalk...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/utils.R (line 70, column 5)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
times)
suppressMessages() in R/fileio.R (line 8, column 5)
suppressMessages() in R/fileio.R (line 15, column 5)
suppressWarnings() in R/pcst.R (line 130, column 9)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 5 functions > 50 lines.
The longest 5 functions are:
run_cytotalk() (R/cytotalk.R, line 70): 229 lines
graph_pathway() (R/graphing.R, line 110): 85 lines
run_pcst() (R/pcst.R, line 9): 83 lines
integrate_network() (R/integrated.R, line 138): 75 lines
analyze_pathway() (R/analysis.R, line 84): 51 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
from_single_cell_experiment.Rd
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 9 lines (0%) are > 80 characters
long.
First 6 lines:
R/analysis.R:76 #' result <- analyze_pathway(df_net_sub, lst_net, cell_...
man/analyze_pathway.Rd:46 result <- analyze_pathway(df_net_sub, lst_net...
man/doc_integrated.Rd:66 \code{parmigene::aracne.m} on the result of \c...
man/doc_pcst.Rd:35 \item{omega_max}{End point of range between \code{om...
man/run_cytotalk.Rd:60 \item{omega_max}{End point of range between \cod...
vignettes/cytotalk_guide.Rmd:28 <img src="https://raw.githubusercontent...
* NOTE: Consider multiples of 4 spaces for line indents, 43
lines(1%) are not.
First 6 lines:
man/doc_integrated.Rd:19 mat_pem,
man/doc_integrated.Rd:20 cell_type_a,
man/doc_integrated.Rd:21 cell_type_b,
man/doc_integrated.Rd:22 vec_nst_a,
man/doc_integrated.Rd:23 vec_nst_b,
man/doc_integrated.Rd:24 mat_type,
See http://bioconductor.org/developers/how-to/coding-style/
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.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 9
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
nebbiolo1 BUILD BIN output
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merida1 Summary
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| Package: CytoTalk |
| Version: 0.99.9 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CytoTalk |
| BuildTime: 0 minutes 7.55 seconds |
| CheckCommand: BiocCheckGitClone('CytoTalk') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CytoTalk_0.99.9.tar.gz && BiocCheck('CytoTalk_0.99.9.tar.gz', `new-package`=TRUE) |
| CheckTime: 1 minutes 51.06 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh CytoTalk_0.99.9.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 5.59 seconds |
| PackageFileSize: 4680.99 KiB |
| BuildID:: CytoTalk_20220225191204 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: CytoTalk. 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. Checking Package status: 0. Build Package status: 0. |
merida1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘CytoTalk/DESCRIPTION’ ... OK
* preparing ‘CytoTalk’:
* 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
* building ‘CytoTalk_0.99.9.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('CytoTalk')
===============================
This is BiocCheckGitClone version 1.31.34. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2508/68e83f2ac1e607335234ec9ba4c0d79a5abc5260/CytoTalk.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CytoTalk/DESCRIPTION’ ... OK
* this is package ‘CytoTalk’ version ‘0.99.9’
* 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 ‘CytoTalk’ can be installed ... [5s/5s] OK
* checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
data 4.3Mb
doc 1.2Mb
* 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 R 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 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 ... [4s/4s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [75s/75s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
doc_mutinfo 63.326 0.105 63.430
doc_integrated 6.882 0.187 7.068
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [1s/1s]
[1s/1s] 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 ... OK
* DONE
Status: 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2508/68e83f2ac1e607335234ec9ba4c0d79a5abc5260/CytoTalk.Rcheck/00check.log’
for details.
===============================
BiocCheck('CytoTalk_0.99.9.tar.gz')
===============================
This is BiocCheck version 1.31.34. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2508/68e83f2ac1e607335234ec9ba4c0d79a5abc5260/CytoTalk_0.99.9.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpyANehf/file151b8487f88a2/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 3.5.0 to 4.2.0.
* 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...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of CytoTalk...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/utils.R (line 70, column 5)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
times)
suppressMessages() in R/fileio.R (line 8, column 5)
suppressMessages() in R/fileio.R (line 15, column 5)
suppressWarnings() in R/pcst.R (line 130, column 9)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 5 functions > 50 lines.
The longest 5 functions are:
run_cytotalk() (R/cytotalk.R, line 70): 229 lines
graph_pathway() (R/graphing.R, line 110): 85 lines
run_pcst() (R/pcst.R, line 9): 83 lines
integrate_network() (R/integrated.R, line 138): 75 lines
analyze_pathway() (R/analysis.R, line 84): 51 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
from_single_cell_experiment.Rd
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 9 lines (0%) are > 80 characters
long.
First 6 lines:
R/analysis.R:76 #' result <- analyze_pathway(df_net_sub, lst_net, cell_...
man/analyze_pathway.Rd:46 result <- analyze_pathway(df_net_sub, lst_net...
man/doc_integrated.Rd:66 \code{parmigene::aracne.m} on the result of \c...
man/doc_pcst.Rd:35 \item{omega_max}{End point of range between \code{om...
man/run_cytotalk.Rd:60 \item{omega_max}{End point of range between \cod...
vignettes/cytotalk_guide.Rmd:28 <img src="https://raw.githubusercontent...
* NOTE: Consider multiples of 4 spaces for line indents, 43
lines(1%) are not.
First 6 lines:
man/doc_integrated.Rd:19 mat_pem,
man/doc_integrated.Rd:20 cell_type_a,
man/doc_integrated.Rd:21 cell_type_b,
man/doc_integrated.Rd:22 vec_nst_a,
man/doc_integrated.Rd:23 vec_nst_b,
man/doc_integrated.Rd:24 mat_type,
See http://bioconductor.org/developers/how-to/coding-style/
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.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 9
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
merida1 BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir CytoTalk_0.99.9.tar.gz'
>>>>>>>
* installing *source* package ‘CytoTalk’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (CytoTalk)