nebbiolo1 Summary
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| Package: updateObject |
| Version: 0.99.6 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data updateObject |
| BuildTime: 0 minutes 13.41 seconds |
| CheckCommand: |
| CheckTime: |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: -1.00 KiB |
| BuildID:: updateObject_20220217082909 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: updateObject. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 1. |
nebbiolo1 BUILD SRC output
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R CMD BUILD
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* checking for file ‘updateObject/DESCRIPTION’ ... OK
* preparing ‘updateObject’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘updateObject.Rmd’ using rmarkdown
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Quitting from lines 132-134 (updateObject.Rmd)
Error: processing vignette 'updateObject.Rmd' failed with diagnostics:
Command:
/usr/bin/git commit -a -m "Pass serialized S4 instances thru updateObject()"
returned error code 128.
--- failed re-building ‘updateObject.Rmd’
SUMMARY: processing the following file failed:
‘updateObject.Rmd’
Error: Vignette re-building failed.
Execution halted
nebbiolo1 CHECK output
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nebbiolo1 BUILD BIN output
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merida1 Summary
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| Package: updateObject |
| Version: 0.99.6 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data updateObject |
| BuildTime: 0 minutes 58.54 seconds |
| CheckCommand: BiocCheckGitClone('updateObject') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch updateObject_0.99.6.tar.gz && BiocCheck('updateObject_0.99.6.tar.gz', `new-package`=TRUE) |
| CheckTime: 3 minutes 12.00 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh updateObject_0.99.6.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 16.90 seconds |
| PackageFileSize: 1198.90 KiB |
| BuildID:: updateObject_20220217082909 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: updateObject. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. 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 ‘updateObject/DESCRIPTION’ ... OK
* preparing ‘updateObject’:
* 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 ‘updateObject_0.99.6.tar.gz’
merida1 CHECK output
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===============================
BiocCheckGitClone('updateObject')
===============================
This is BiocCheckGitClone version 1.31.34. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
inst/scripts/find_serialized_DataFrame_instances-20211119.log
inst/scripts/find_serialized_DataFrame_instances-20220113.log
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 1
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
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2507/updateObject_20220217082909/updateObject.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 ‘updateObject/DESCRIPTION’ ... OK
* this is package ‘updateObject’ version ‘0.99.6’
* 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 ‘updateObject’ can be installed ... [9s/15s] 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 ... [11s/21s] OK
* checking Rd files ... [1s/1s] 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 ... [19s/42s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
updateBiocPackageRepoObjects 11.128 1.028 22.789
git-utils 0.153 0.178 6.770
* 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('updateObject_0.99.6.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/2507/updateObject_20220217082909/updateObject_0.99.6.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpxEuMkE/file167ad7d626e94/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...
* 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 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 vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of updateObject...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/git-utils.R (line 59, column 13)
cat() in R/git-utils.R (line 65, column 9)
cat() in R/git-utils.R (line 177, column 5)
cat() in R/git-utils.R (line 200, column 9)
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/git-utils.R (line 68, column 14)
R/updateBiocPackageRepoObjects.R (line 34, column 14)
R/updateSerializedObjects.R (line 122, column 17)
R/updateSerializedObjects.R (line 169, column 21)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 14
times)
suppressWarnings() in R/git-utils.R (line 26, column 20)
suppressWarnings() in R/git-utils.R (line 49, column 16)
suppressWarnings() in R/git-utils.R (line 51, column 19)
suppressWarnings() in R/git-utils.R (line 56, column 19)
suppressWarnings() in R/updatePackageObjects.R (line 19, column
9)
suppressWarnings() in R/updateSerializedObjects.R (line 64,
column 26)
suppressWarnings() in R/updateSerializedObjects.R (line 86,
column 20)
suppressWarnings() in R/updateSerializedObjects.R (line 90,
column 20)
suppressWarnings() in R/updateSerializedObjects.R (line 147,
column 26)
suppressWarnings() in R/updateSerializedObjects.R (line 165,
column 26)
suppressMessages() in R/updateSerializedObjects.R (line 64,
column 9)
suppressMessages() in R/updateSerializedObjects.R (line 85,
column 9)
suppressMessages() in R/updateSerializedObjects.R (line 147,
column 9)
suppressMessages() in R/updateSerializedObjects.R (line 165,
column 9)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 2 functions > 50 lines.
The longest 5 functions are:
updateBiocPackageRepoObjects()
(R/updateBiocPackageRepoObjects.R, line 7): 57 lines
update_rda_file() (R/updateSerializedObjects.R, line 142): 53
lines
find_python() (R/find_python.R, line 2): 39 lines
.find_git() (R/git-utils.R, line 8): 31 lines
update_rds_file() (R/updateSerializedObjects.R, line 110): 31
lines
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
40% of man pages use one of these cases.
Found in the following files:
updateBiocPackageRepoObjects.Rd
updatePackageObjects.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
updateBiocPackageRepoObjects.Rd
updatePackageObjects.Rd
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider multiples of 4 spaces for line indents, 262
lines(16%) are not.
First 6 lines:
R/bump_pkg_version.R:52 "to the top-level directory o...
R/bump_pkg_version.R:62 "an R package **source** t...
R/bump_pkg_version.R:65 "it is an R package **inst...
R/bump_pkg_version.R:66 "or the result of extracti...
R/bump_pkg_version.R:81 function(val) paste0(" ", ...
R/find_python.R:14 stop("\n No Python executable can be f...
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
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir updateObject_0.99.6.tar.gz'
>>>>>>>
* installing *source* package ‘updateObject’ ...
** 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 (updateObject)