merida1 Summary
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Package: crisprDesign |
Version: 0.99.78 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data crisprDesign |
BuildTime: 1 minutes 34.65 seconds |
CheckCommand: BiocCheckGitClone('crisprDesign') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch crisprDesign_0.99.78.tar.gz && BiocCheck('crisprDesign_0.99.78.tar.gz', `new-package`=TRUE) |
CheckTime: 10 minutes 41.97 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh crisprDesign_0.99.78.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 51.52 seconds |
PackageFileSize: 1200.56 KiB |
BuildID:: crisprDesign_20220512174259 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: crisprDesign. 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 ‘crisprDesign/DESCRIPTION’ ... OK
* preparing ‘crisprDesign’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘crisprDesign_0.99.78.tar.gz’
merida1 CHECK output
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===============================
BiocCheckGitClone('crisprDesign')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: crisprDesign
─ PackageVersion: 0.99.78
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2647/crisprDesign_20220512174259/crisprDesign
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2647/crisprDesign_20220512174259/crisprDesign.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crisprDesign/DESCRIPTION’ ... OK
* this is package ‘crisprDesign’ version ‘0.99.78’
* 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 ‘crisprDesign’ can be installed ... [52s/53s] 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 ... [52s/53s] 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 ... WARNING
Error loading dataset 'guideSetExample':
Error in .requirePackage(package) :
unable to find required package 'crisprDesign'
Error loading dataset 'guideSetExampleFullAnnotation':
Error in .requirePackage(package) :
unable to find required package 'crisprDesign'
Error loading dataset 'guideSetExampleWithAlignments':
Error in .requirePackage(package) :
unable to find required package 'crisprDesign'
The dataset(s) may use package(s) not declared in Depends/Imports.
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [65s/65s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
addEditedAlleles 11.957 0.303 12.259
addSNPAnnotation 11.832 0.033 11.864
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [146s/153s]
[147s/154s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (73)
• long run time (8)
• no del for guideSetExample (1)
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-addSpacerAlignments.R:2:1): (code run outside of `test_that()`) ──
<packageNotFoundError/error/condition>
Error in `library(crisprDesignData)`: there is no package called 'crisprDesignData'
Backtrace:
▆
1. └─base::library(crisprDesignData) at test-addSpacerAlignments.R:2:0
── Error (test-getMrnaSequence.R:1:1): (code run outside of `test_that()`) ─────
<packageNotFoundError/error/condition>
Error in `library("crisprDesignData")`: there is no package called 'crisprDesignData'
Backtrace:
▆
1. └─base::library("crisprDesignData") at test-getMrnaSequence.R:1:0
[ FAIL 2 | WARN 0 | SKIP 82 | PASS 853 ]
Error: Test failures
Execution halted
* 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 ERROR, 1 WARNING
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2647/crisprDesign_20220512174259/crisprDesign.Rcheck/00check.log’
for details.
===============================
BiocCheck('crisprDesign_0.99.78.tar.gz')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: crisprDesign
─ PackageVersion: 0.99.78
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpXJw5rG/filed0d759d50b3a/crisprDesign
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpXJw5rG/filed0d76467b08d
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2647/crisprDesign_20220512174259/crisprDesign.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
snapshotDate(): 2022-04-26
* 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...
* 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 crisprDesign...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 15
functions > 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
documentexported objects.
* 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; 51 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1288 lines
(11%) are not.
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.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 5 NOTES
See the crisprDesign.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
merida1 BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir crisprDesign_0.99.78.tar.gz'
>>>>>>>
* installing *source* package ‘crisprDesign’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
snapshotDate(): 2022-04-26
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
snapshotDate(): 2022-04-26
** testing if installed package can be loaded from final location
snapshotDate(): 2022-04-26
** testing if installed package keeps a record of temporary installation path
* DONE (crisprDesign)
nebbiolo1 Summary
[top]
Package: crisprDesign |
Version: 0.99.78 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data crisprDesign |
BuildTime: 1 minutes 3.38 seconds |
CheckCommand: BiocCheckGitClone('crisprDesign') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings crisprDesign_0.99.78.tar.gz && BiocCheck('crisprDesign_0.99.78.tar.gz', `new-package`=TRUE) |
CheckTime: 6 minutes 56.47 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 1200.61 KiB |
BuildID:: crisprDesign_20220512174259 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: crisprDesign. 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
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘crisprDesign/DESCRIPTION’ ... OK
* preparing ‘crisprDesign’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘crisprDesign_0.99.78.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('crisprDesign')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: crisprDesign
─ PackageVersion: 0.99.78
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2647/crisprDesign_20220512174259/crisprDesign
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2647/crisprDesign_20220512174259/crisprDesign.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crisprDesign/DESCRIPTION’ ... OK
* this is package ‘crisprDesign’ version ‘0.99.78’
* 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 ‘crisprDesign’ can be installed ... [36s/37s] 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 ... [34s/35s] 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 ... WARNING
Error loading dataset 'guideSetExample':
Error in .requirePackage(package) :
unable to find required package 'crisprDesign'
Error loading dataset 'guideSetExampleFullAnnotation':
Error in .requirePackage(package) :
unable to find required package 'crisprDesign'
Error loading dataset 'guideSetExampleWithAlignments':
Error in .requirePackage(package) :
unable to find required package 'crisprDesign'
The dataset(s) may use package(s) not declared in Depends/Imports.
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [49s/49s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
addEditedAlleles 7.658 0.316 7.975
addSNPAnnotation 7.267 0.064 7.331
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [95s/97s]
[96s/97s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (73)
• long run time (8)
• no del for guideSetExample (1)
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-addSpacerAlignments.R:2:1): (code run outside of `test_that()`) ──
<packageNotFoundError/error/condition>
Error in `library(crisprDesignData)`: there is no package called 'crisprDesignData'
Backtrace:
▆
1. └─base::library(crisprDesignData) at test-addSpacerAlignments.R:2:0
── Error (test-getMrnaSequence.R:1:1): (code run outside of `test_that()`) ─────
<packageNotFoundError/error/condition>
Error in `library("crisprDesignData")`: there is no package called 'crisprDesignData'
Backtrace:
▆
1. └─base::library("crisprDesignData") at test-getMrnaSequence.R:1:0
[ FAIL 2 | WARN 0 | SKIP 82 | PASS 853 ]
Error: Test failures
Execution halted
* 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 ERROR, 1 WARNING
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2647/crisprDesign_20220512174259/crisprDesign.Rcheck/00check.log’
for details.
===============================
BiocCheck('crisprDesign_0.99.78.tar.gz')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: crisprDesign
─ PackageVersion: 0.99.78
─ sourceDir: /tmp/Rtmp5BQ2rY/file2590904ae59c6b/crisprDesign
─ installDir: /tmp/Rtmp5BQ2rY/file25909059fe0eae
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2647/crisprDesign_20220512174259/crisprDesign.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
snapshotDate(): 2022-04-26
* 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...
* 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 crisprDesign...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 15
functions > 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
documentexported objects.
* 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; 51 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1288 lines
(11%) are not.
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.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 5 NOTES
See the crisprDesign.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
[top]