nebbiolo1 Summary
[top]
Package: goSorensen |
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 goSorensen |
BuildTime: 3 minutes 35.41 seconds |
CheckCommand: BiocCheckGitClone('goSorensen') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings goSorensen_0.99.6.tar.gz && BiocCheck('goSorensen_0.99.6.tar.gz', `new-package`=TRUE) |
CheckTime: 3 minutes 58.11 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 331.39 KiB |
BuildID:: goSorensen_20220523152724 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: goSorensen. 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 ‘goSorensen/DESCRIPTION’ ... OK
* preparing ‘goSorensen’:
* 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 ‘goSorensen_0.99.6.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('goSorensen')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: goSorensen
─ PackageVersion: 0.99.6
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2658/a9fb424296bec711c6a9942318efd6a7949cf1c1/goSorensen
─ 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/2658/a9fb424296bec711c6a9942318efd6a7949cf1c1/goSorensen.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 ‘goSorensen/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘goSorensen’ 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 ‘goSorensen’ can be installed ... [17s/17s] 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 ... [18s/18s] 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 ... [25s/25s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
buildEnrichTable 10.464 0.57 11.06
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test_gosorensen_funcs.R’ [84s/84s]
[84s/84s] 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 ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Missing $ inserted.
<inserted text>
$
l.433 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.433 }
! Missing $ inserted.
<inserted text>
$
l.433 }
! Missing } inserted.
<inserted text>
}
l.433 }
! Missing $ inserted.
<inserted text>
$
l.433 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.433 }
! Missing $ inserted.
<inserted text>
$
l.433 }
! Missing } inserted.
<inserted text>
}
l.433 }
! Missing $ inserted.
<inserted text>
$
l.433 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.433 }
! Missing $ inserted.
<inserted text>
$
l.433 }
! Missing } inserted.
<inserted text>
}
l.433 }
! Missing $ inserted.
<inserted text>
$
l.433 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.433 }
! Missing $ inserted.
<inserted text>
$
l.433 }
! Missing } inserted.
<inserted text>
}
l.433 }
! Missing $ inserted.
<inserted text>
$
l.652 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.652 }
! Missing $ inserted.
<inserted text>
$
l.652 }
! Missing } inserted.
<inserted text>
}
l.652 }
! Missing $ inserted.
<inserted text>
$
l.652 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.652 }
! Missing $ inserted.
<inserted text>
$
l.652 }
! Missing } inserted.
<inserted text>
}
l.652 }
! Missing $ inserted.
<inserted text>
$
l.652 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.652 }
! Missing $ inserted.
<inserted text>
$
l.652 }
! Missing } inserted.
<inserted text>
}
l.652 }
! Missing $ inserted.
<inserted text>
$
l.652 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.652 }
! Missing $ inserted.
<inserted text>
$
l.652 }
! Missing } inserted.
<inserted text>
}
l.652 }
! Missing $ inserted.
<inserted text>
$
l.861 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.861 }
! Missing $ inserted.
<inserted text>
$
l.861 }
! Missing } inserted.
<inserted text>
}
l.861 }
! Missing $ inserted.
<inserted text>
$
l.861 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.861 }
! Missing $ inserted.
<inserted text>
$
l.861 }
! Missing } inserted.
<inserted text>
}
l.861 }
! Missing $ inserted.
<inserted text>
$
l.861 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.861 }
! Missing $ inserted.
<inserted text>
$
l.861 }
! Missing } inserted.
<inserted text>
}
l.861 }
! Missing $ inserted.
<inserted text>
$
l.861 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.861 }
! Missing $ inserted.
<inserted text>
$
l.861 }
! Missing } inserted.
<inserted text>
}
l.861 }
! Missing $ inserted.
<inserted text>
$
l.1857 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.1857 }
! Missing $ inserted.
<inserted text>
$
l.1857 }
! Missing } inserted.
<inserted text>
}
l.1857 }
! Missing $ inserted.
<inserted text>
$
l.1857 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.1857 }
! Missing $ inserted.
<inserted text>
$
l.1857 }
! Missing } inserted.
<inserted text>
}
l.1857 }
! Missing $ inserted.
<inserted text>
$
l.1857 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.1857 }
! Missing $ inserted.
<inserted text>
$
l.1857 }
! Missing } inserted.
<inserted text>
}
l.1857 }
! Missing $ inserted.
<inserted text>
$
l.1857 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.1857 }
! Missing $ inserted.
<inserted text>
$
l.1857 }
! Missing } inserted.
<inserted text>
}
l.1857 }
! Missing $ inserted.
<inserted text>
$
l.2040 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.2040 }
! Missing $ inserted.
<inserted text>
$
l.2040 }
! Missing } inserted.
<inserted text>
}
l.2040 }
! Missing $ inserted.
<inserted text>
$
l.2040 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.2040 }
! Missing $ inserted.
<inserted text>
$
l.2040 }
! Missing } inserted.
<inserted text>
}
l.2040 }
! Missing $ inserted.
<inserted text>
$
l.2040 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.2040 }
! Missing $ inserted.
<inserted text>
$
l.2040 }
! Missing } inserted.
<inserted text>
}
l.2040 }
! Missing $ inserted.
<inserted text>
$
l.2040 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.2040 }
! Missing $ inserted.
<inserted text>
$
l.2040 }
! Missing } inserted.
<inserted text>
}
l.2040 }
* checking PDF version of manual without index ... ERROR
* DONE
Status: 1 ERROR, 1 WARNING
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2658/a9fb424296bec711c6a9942318efd6a7949cf1c1/goSorensen.Rcheck/00check.log’
for details.
===============================
BiocCheck('goSorensen_0.99.6.tar.gz')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: goSorensen
─ PackageVersion: 0.99.6
─ sourceDir: /tmp/RtmpJJGkUY/file12bbb213026857/goSorensen
─ installDir: /tmp/RtmpJJGkUY/file12bbb223830f8a
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2658/a9fb424296bec711c6a9942318efd6a7949cf1c1/goSorensen.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* 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...
* 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...
* 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...
* NOTE: Consider adding these automatically suggested biocViews:
Reactome, Clustering, KEGG
Search 'biocViews' at https://contributions.bioconductor.org
* 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...
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of goSorensen...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 5
functions > 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
documentexported objects.
* 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; 816 lines (17%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 931 lines
(19%) 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 | 13 NOTES
See the goSorensen.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
[top]
merida1 Summary
[top]
Package: goSorensen |
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 goSorensen |
BuildTime: 4 minutes 39.03 seconds |
CheckCommand: BiocCheckGitClone('goSorensen') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch goSorensen_0.99.6.tar.gz && BiocCheck('goSorensen_0.99.6.tar.gz', `new-package`=TRUE) |
CheckTime: 5 minutes 44.97 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh goSorensen_0.99.6.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 24.91 seconds |
PackageFileSize: 332.35 KiB |
BuildID:: goSorensen_20220523152724 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: goSorensen. 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
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘goSorensen/DESCRIPTION’ ... OK
* preparing ‘goSorensen’:
* 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 ‘goSorensen_0.99.6.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('goSorensen')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: goSorensen
─ PackageVersion: 0.99.6
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2658/a9fb424296bec711c6a9942318efd6a7949cf1c1/goSorensen
─ 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/2658/a9fb424296bec711c6a9942318efd6a7949cf1c1/goSorensen.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 ‘goSorensen/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘goSorensen’ 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 ‘goSorensen’ can be installed ... [25s/25s] 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 ... [27s/27s] 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 ... [34s/34s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
buildEnrichTable 14.6 0.905 15.706
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test_gosorensen_funcs.R’ [109s/109s]
[109s/109s] 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 ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Missing $ inserted.
<inserted text>
$
l.433 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.433 }
! Missing $ inserted.
<inserted text>
$
l.433 }
! Missing } inserted.
<inserted text>
}
l.433 }
! Missing $ inserted.
<inserted text>
$
l.433 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.433 }
! Missing $ inserted.
<inserted text>
$
l.433 }
! Missing } inserted.
<inserted text>
}
l.433 }
! Missing $ inserted.
<inserted text>
$
l.433 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.433 }
! Missing $ inserted.
<inserted text>
$
l.433 }
! Missing } inserted.
<inserted text>
}
l.433 }
! Missing $ inserted.
<inserted text>
$
l.433 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.433 }
! Missing $ inserted.
<inserted text>
$
l.433 }
! Missing } inserted.
<inserted text>
}
l.433 }
! Missing $ inserted.
<inserted text>
$
l.652 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.652 }
! Missing $ inserted.
<inserted text>
$
l.652 }
! Missing } inserted.
<inserted text>
}
l.652 }
! Missing $ inserted.
<inserted text>
$
l.652 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.652 }
! Missing $ inserted.
<inserted text>
$
l.652 }
! Missing } inserted.
<inserted text>
}
l.652 }
! Missing $ inserted.
<inserted text>
$
l.652 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.652 }
! Missing $ inserted.
<inserted text>
$
l.652 }
! Missing } inserted.
<inserted text>
}
l.652 }
! Missing $ inserted.
<inserted text>
$
l.652 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.652 }
! Missing $ inserted.
<inserted text>
$
l.652 }
! Missing } inserted.
<inserted text>
}
l.652 }
! Missing $ inserted.
<inserted text>
$
l.861 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.861 }
! Missing $ inserted.
<inserted text>
$
l.861 }
! Missing } inserted.
<inserted text>
}
l.861 }
! Missing $ inserted.
<inserted text>
$
l.861 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.861 }
! Missing $ inserted.
<inserted text>
$
l.861 }
! Missing } inserted.
<inserted text>
}
l.861 }
! Missing $ inserted.
<inserted text>
$
l.861 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.861 }
! Missing $ inserted.
<inserted text>
$
l.861 }
! Missing } inserted.
<inserted text>
}
l.861 }
! Missing $ inserted.
<inserted text>
$
l.861 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.861 }
! Missing $ inserted.
<inserted text>
$
l.861 }
! Missing } inserted.
<inserted text>
}
l.861 }
! Missing $ inserted.
<inserted text>
$
l.1857 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.1857 }
! Missing $ inserted.
<inserted text>
$
l.1857 }
! Missing } inserted.
<inserted text>
}
l.1857 }
! Missing $ inserted.
<inserted text>
$
l.1857 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.1857 }
! Missing $ inserted.
<inserted text>
$
l.1857 }
! Missing } inserted.
<inserted text>
}
l.1857 }
! Missing $ inserted.
<inserted text>
$
l.1857 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.1857 }
! Missing $ inserted.
<inserted text>
$
l.1857 }
! Missing } inserted.
<inserted text>
}
l.1857 }
! Missing $ inserted.
<inserted text>
$
l.1857 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.1857 }
! Missing $ inserted.
<inserted text>
$
l.1857 }
! Missing } inserted.
<inserted text>
}
l.1857 }
! Missing $ inserted.
<inserted text>
$
l.2040 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.2040 }
! Missing $ inserted.
<inserted text>
$
l.2040 }
! Missing } inserted.
<inserted text>
}
l.2040 }
! Missing $ inserted.
<inserted text>
$
l.2040 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.2040 }
! Missing $ inserted.
<inserted text>
$
l.2040 }
! Missing } inserted.
<inserted text>
}
l.2040 }
! Missing $ inserted.
<inserted text>
$
l.2040 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.2040 }
! Missing $ inserted.
<inserted text>
$
l.2040 }
! Missing } inserted.
<inserted text>
}
l.2040 }
! Missing $ inserted.
<inserted text>
$
l.2040 }
! LaTeX Error: Bad math environment delimiter.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Extra }, or forgotten $.
<template> \unskip }
\hskip \tabcolsep \endtemplate
l.2040 }
! Missing $ inserted.
<inserted text>
$
l.2040 }
! Missing } inserted.
<inserted text>
}
l.2040 }
* checking PDF version of manual without index ... ERROR
* DONE
Status: 1 ERROR, 1 WARNING
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2658/a9fb424296bec711c6a9942318efd6a7949cf1c1/goSorensen.Rcheck/00check.log’
for details.
===============================
BiocCheck('goSorensen_0.99.6.tar.gz')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: goSorensen
─ PackageVersion: 0.99.6
─ sourceDir: /tmp/RtmpDXeBdD/file1279631b15f28/goSorensen
─ installDir: /tmp/RtmpDXeBdD/file12796982fbfa
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2658/a9fb424296bec711c6a9942318efd6a7949cf1c1/goSorensen.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* 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...
* 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...
* 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...
* NOTE: Consider adding these automatically suggested biocViews:
Reactome, Clustering, KEGG
Search 'biocViews' at https://contributions.bioconductor.org
* 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...
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of goSorensen...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 5
functions > 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
documentexported objects.
* 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; 816 lines (17%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 931 lines
(19%) 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 | 13 NOTES
See the goSorensen.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir goSorensen_0.99.6.tar.gz'
>>>>>>>
* installing *source* package ‘goSorensen’ ...
** 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 (goSorensen)