merida1 Summary
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Package: lineagespot |
Version: 0.99.11 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data lineagespot |
BuildTime: 2 minutes 3.67 seconds |
CheckCommand: BiocCheckGitClone('lineagespot') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lineagespot_0.99.11.tar.gz && BiocCheck('lineagespot_0.99.11.tar.gz', `new-package`=TRUE) |
CheckTime: 10 minutes 58.61 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh lineagespot_0.99.11.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 1 minutes 1.80 seconds |
PackageFileSize: 5086.97 KiB |
BuildID:: lineagespot_20220113093322 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: lineagespot. 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: 1. Build Package status: 0. |
merida1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘lineagespot/DESCRIPTION’ ... OK
* preparing ‘lineagespot’:
* 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 ‘lineagespot_0.99.11.tar.gz’
merida1 CHECK output
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===============================
BiocCheckGitClone('lineagespot')
===============================
This is BiocCheckGitClone version 1.31.23. 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/2314/6cd32845d54ff26816d4676717f73a27c19fb1c5/lineagespot.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 ‘lineagespot/DESCRIPTION’ ... OK
* this is package ‘lineagespot’ version ‘0.99.11’
* 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 ‘lineagespot’ can be installed ... [61s/61s] OK
* checking installed package size ... NOTE
installed size is 9.6Mb
sub-directories of 1Mb or more:
extdata 8.6Mb
* 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 ... [62s/63s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [112s/113s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
lineagespot 23.078 0.470 23.598
uniq_variants 22.755 0.211 23.988
lineagespot_hits 20.737 0.180 21.044
merge_vcf 17.426 0.115 17.569
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [93s/94s]
[93s/95s] 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/2314/6cd32845d54ff26816d4676717f73a27c19fb1c5/lineagespot.Rcheck/00check.log’
for details.
===============================
BiocCheck('lineagespot_0.99.11.tar.gz')
===============================
This is BiocCheck version 1.31.23. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* 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...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* Checking package size...
* ERROR: Package Source tarball exceeds Bioconductor size
requirement.
Package Size: 5.2091 MB
Size Requirement: 5.0000 MB
* 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 lineagespot...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 5 functions > 50 lines.
The longest 5 functions are:
lineagespot_hits() (R/lineagespot_hits.R, line 48): 247 lines
uniq_variants() (R/uniq_variants.R, line 47): 90 lines
vcf_to_table() (R/merge_vcf.R, line 97): 65 lines
change_AA_abbreviations() (R/merge_vcf.R, line 208): 62 lines
merge_vcf() (R/merge_vcf.R, line 35): 61 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
get_lineage_report.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
12% of man pages use one of these cases.
Found in the following files:
get_lineage_report.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
get_lineage_report.Rd
* 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; 6 lines (0%) are > 80 characters
long.
First 6 lines:
man/get_lineage_report.Rd:9 base.url = "https://api.outbreak.info/gen...
man/get_lineage_report.Rd:13 \item{lineages}{a character vector contain...
man/lineagespot_hits.Rd:14 \item{vcf_table}{A tab-delimited table conta...
man/lineagespot.Rd:28 \item{AF_threshold}{A parameter indicating the AF...
man/uniq_variants.Rd:10 \item{hits_table}{A tab-delimited table contain...
man/uniq_variants.Rd:14 \item{AF_threshold}{A parameter indicating the ...
* NOTE: Consider multiples of 4 spaces for line indents, 90
lines(5%) are not.
First 6 lines:
R/input_checking.R:36 vcf_folder = NULL,
R/input_checking.R:37 gff3_path = NULL) {
R/input_checking.R:38 if (is.null(vcf_fls) & is.null(vcf_folder)) {
R/input_checking.R:40 } else if (!is.null(vcf_fls) & !is.null(vcf_fol...
R/input_checking.R:42 "Please give only one source for VCF. ",
R/input_checking.R:43 "Other a vector of paths to VCF files",
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: 1
WARNING count: 0
NOTE count: 6
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
BiocCheck FAILED.
merida1 BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir lineagespot_0.99.11.tar.gz'
>>>>>>>
* installing *source* package ‘lineagespot’ ...
** 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 (lineagespot)
nebbiolo1 Summary
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Package: lineagespot |
Version: 0.99.11 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data lineagespot |
BuildTime: 0 minutes 42.40 seconds |
CheckCommand: BiocCheckGitClone('lineagespot') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings lineagespot_0.99.11.tar.gz && BiocCheck('lineagespot_0.99.11.tar.gz', `new-package`=TRUE) |
CheckTime: 4 minutes 18.82 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 5087.06 KiB |
BuildID:: lineagespot_20220113093322 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: lineagespot. 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: 1. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘lineagespot/DESCRIPTION’ ... OK
* preparing ‘lineagespot’:
* 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 ‘lineagespot_0.99.11.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('lineagespot')
===============================
This is BiocCheckGitClone version 1.31.23. 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/2314/6cd32845d54ff26816d4676717f73a27c19fb1c5/lineagespot.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lineagespot/DESCRIPTION’ ... OK
* this is package ‘lineagespot’ version ‘0.99.11’
* 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 ‘lineagespot’ can be installed ... [23s/23s] OK
* checking installed package size ... NOTE
installed size is 6.0Mb
sub-directories of 1Mb or more:
extdata 5.3Mb
* 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 ... [24s/24s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [50s/44s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
uniq_variants 10.679 0.171 8.390
lineagespot 10.210 0.385 8.347
lineagespot_hits 8.583 0.186 7.804
merge_vcf 6.791 0.096 6.869
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [40s/35s]
[40s/35s] 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
‘/home/pkgbuild/packagebuilder/workers/jobs/2314/6cd32845d54ff26816d4676717f73a27c19fb1c5/lineagespot.Rcheck/00check.log’
for details.
===============================
BiocCheck('lineagespot_0.99.11.tar.gz')
===============================
This is BiocCheck version 1.31.23. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* 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...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* Checking package size...
* ERROR: Package Source tarball exceeds Bioconductor size
requirement.
Package Size: 5.2091 MB
Size Requirement: 5.0000 MB
* 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 lineagespot...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 5 functions > 50 lines.
The longest 5 functions are:
lineagespot_hits() (R/lineagespot_hits.R, line 48): 247 lines
uniq_variants() (R/uniq_variants.R, line 47): 90 lines
vcf_to_table() (R/merge_vcf.R, line 97): 65 lines
change_AA_abbreviations() (R/merge_vcf.R, line 208): 62 lines
merge_vcf() (R/merge_vcf.R, line 35): 61 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
get_lineage_report.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
12% of man pages use one of these cases.
Found in the following files:
get_lineage_report.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
get_lineage_report.Rd
* 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; 6 lines (0%) are > 80 characters
long.
First 6 lines:
man/get_lineage_report.Rd:9 base.url = "https://api.outbreak.info/gen...
man/get_lineage_report.Rd:13 \item{lineages}{a character vector contain...
man/lineagespot_hits.Rd:14 \item{vcf_table}{A tab-delimited table conta...
man/lineagespot.Rd:28 \item{AF_threshold}{A parameter indicating the AF...
man/uniq_variants.Rd:10 \item{hits_table}{A tab-delimited table contain...
man/uniq_variants.Rd:14 \item{AF_threshold}{A parameter indicating the ...
* NOTE: Consider multiples of 4 spaces for line indents, 90
lines(5%) are not.
First 6 lines:
R/input_checking.R:36 vcf_folder = NULL,
R/input_checking.R:37 gff3_path = NULL) {
R/input_checking.R:38 if (is.null(vcf_fls) & is.null(vcf_folder)) {
R/input_checking.R:40 } else if (!is.null(vcf_fls) & !is.null(vcf_fol...
R/input_checking.R:42 "Please give only one source for VCF. ",
R/input_checking.R:43 "Other a vector of paths to VCF files",
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: 1
WARNING count: 0
NOTE count: 6
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
BiocCheck FAILED.
nebbiolo1 BUILD BIN output
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