merida1 Summary
[top]
Package: TEKRABber |
Version: 0.99.0 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data TEKRABber |
BuildTime: 2 minutes 9.04 seconds |
CheckCommand: BiocCheckGitClone('TEKRABber') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch TEKRABber_0.99.0.tar.gz && BiocCheck('TEKRABber_0.99.0.tar.gz', `new-package`=TRUE) |
CheckTime: 4 minutes 50.55 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh TEKRABber_0.99.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 32.29 seconds |
PackageFileSize: 2685.14 KiB |
BuildID:: TEKRABber_20220113185942 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: TEKRABber. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘TEKRABber/DESCRIPTION’ ... OK
* preparing ‘TEKRABber’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
Warning: ‘inst/doc’ file
‘TEKRABber.html’
ignored as vignettes have been rebuilt.
Run R CMD build with --no-build-vignettes to prevent rebuilding.
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘TEKRABber_0.99.0.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('TEKRABber')
===============================
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/2446/TEKRABber_20220113185942/TEKRABber.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 ‘TEKRABber/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TEKRABber’ version ‘0.99.0’
* 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 ‘TEKRABber’ can be installed ... [31s/31s] 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 ... [22s/22s] NOTE
appTEKRABber : server: no visible binding for global variable ‘group’
appTEKRABber : server: no visible binding for global variable
‘geneName’
appTEKRABber : server: no visible binding for global variable ‘teName’
appTEKRABber : server: no visible binding for global variable ‘padj’
assay_tekcorrset: no visible binding for global variable ‘sepc’
corrOrthologTE: no visible binding for global variable ‘pvalue’
orthologScale: no visible binding for global variable ‘refEnd’
orthologScale: no visible binding for global variable ‘refStart’
orthologScale: no visible binding for global variable ‘compareEnd’
orthologScale: no visible binding for global variable ‘compareStart’
orthologScale: no visible binding for global variable ‘.’
orthologScale: no visible binding for global variable
‘orthologyConfidence’
Undefined global functions or variables:
. compareEnd compareStart geneName group orthologyConfidence padj
pvalue refEnd refStart sepc teName
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'DECorrInputs.Rd':
\usage lines wider than 90 characters:
DECorrInputs(orthologTable, scaleFactor, geneCountRef, geneCountCompare, teCountRef, teCountCompare)
These lines will be truncated in the PDF manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [109s/109s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DEgeneTE 50.644 0.481 51.128
appTEKRABber 47.321 0.217 47.540
* 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: 2 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2446/TEKRABber_20220113185942/TEKRABber.Rcheck/00check.log’
for details.
===============================
BiocCheck('TEKRABber_0.99.0.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...
* NOTE: Consider clarifying how 12 object(s) are initialized. Maybe
they are part of a data set loaded with data(), or perhaps part
of an object referenced in with() or within().
function (object)
appTEKRABber (group)
appTEKRABber (geneName)
appTEKRABber (teName)
appTEKRABber (padj)
assay_tekcorrset (sepc)
corrOrthologTE (pvalue)
orthologScale (refEnd)
orthologScale (refStart)
orthologScale (compareEnd)
orthologScale (compareStart)
orthologScale (.)
orthologScale (orthologyConfidence)
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 4.0 to 4.2.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
GeneExpression
See http://bioconductor.org/developers/how-to/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...
* NOTE: License 'GPL (>= 2)' unknown; licenses cannot restrict use
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/TEKRABber.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of TEKRABber...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
corrOrthologTE.R (line 33, column 23)
corrOrthologTE.R (line 36, column 28)
DECorrInputs.R (line 81, column 43)
DECorrInputs.R (line 83, column 39)
orthologScale.R (line 97, column 55)
* 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:
appTEKRABber() (R/appTEKRABber.R, line 59): 214 lines
server() (R/appTEKRABber.R, line 141): 129 lines
DEgeneTE() (R/DEgeneTE.R, line 34): 90 lines
orthologScale() (R/orthologScale.R, line 22): 84 lines
DECorrInputs() (R/DECorrInputs.R, line 35): 62 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
rcpp_corr.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
8% of man pages use one of these cases.
Found in the following files:
TEKRABber-package.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
TEKRABber-package.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 shorter lines; 143 lines (10%) are > 80 characters
long.
First 6 lines:
R/appTEKRABber.R:2 #' @description To help user explore their results u...
R/appTEKRABber.R:3 #' using a self-written shiny app with two tabs, inc...
R/appTEKRABber.R:7 #' @param corrRef the correlation result of your ref...
R/appTEKRABber.R:8 #' @param corrCompare the correlation result of your...
R/appTEKRABber.R:10 #' @return an app can display differentially expres...
R/appTEKRABber.R:19 #' metaExp$experiment <- factor(metaExp$experiment,...
* NOTE: Consider multiples of 4 spaces for line indents, 66
lines(5%) are not.
First 6 lines:
man/appTEKRABber.Rd:36 geneTable = geneInputDE,
man/appTEKRABber.Rd:37 teTable = teInputDE,
man/appTEKRABber.Rd:38 metadata = metaExp,
man/appTEKRABber.Rd:39 contrastVector = c("experiment", "control", "t...
man/appTEKRABber.Rd:40 expDesign = FALSE
man/assay_tekcorrset.Rd:16 are for running same species design.}
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: 15
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
merida1 BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir TEKRABber_0.99.0.tar.gz'
>>>>>>>
* installing *source* package ‘TEKRABber’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rcpp_corr.cpp -o rcpp_corr.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o TEKRABber.so RcppExports.o rcpp_corr.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/pkgbuild/packagebuilder/workers/jobs/2446/TEKRABber_20220113185942/libdir/00LOCK-TEKRABber/00new/TEKRABber/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TEKRABber)
>>>>>>>
>>>>>>> FIXING LINKS FOR libdir/TEKRABber/libs/TEKRABber.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "libdir/TEKRABber/libs/TEKRABber.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "libdir/TEKRABber/libs/TEKRABber.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "libdir/TEKRABber/libs/TEKRABber.so"
nebbiolo1 Summary
[top]
Package: TEKRABber |
Version: 0.99.0 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data TEKRABber |
BuildTime: 1 minutes 16.86 seconds |
CheckCommand: BiocCheckGitClone('TEKRABber') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings TEKRABber_0.99.0.tar.gz && BiocCheck('TEKRABber_0.99.0.tar.gz', `new-package`=TRUE) |
CheckTime: 3 minutes 11.32 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 2685.13 KiB |
BuildID:: TEKRABber_20220113185942 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: TEKRABber. Starting Build package. Starting Check package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘TEKRABber/DESCRIPTION’ ... OK
* preparing ‘TEKRABber’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
Warning: ‘inst/doc’ file
‘TEKRABber.html’
ignored as vignettes have been rebuilt.
Run R CMD build with --no-build-vignettes to prevent rebuilding.
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘TEKRABber_0.99.0.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('TEKRABber')
===============================
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/2446/TEKRABber_20220113185942/TEKRABber.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 ‘TEKRABber/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TEKRABber’ version ‘0.99.0’
* 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 ‘TEKRABber’ can be installed ... [23s/23s] 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 ... [15s/15s] NOTE
appTEKRABber : server: no visible binding for global variable ‘group’
appTEKRABber : server: no visible binding for global variable
‘geneName’
appTEKRABber : server: no visible binding for global variable ‘teName’
appTEKRABber : server: no visible binding for global variable ‘padj’
assay_tekcorrset: no visible binding for global variable ‘sepc’
corrOrthologTE: no visible binding for global variable ‘pvalue’
orthologScale: no visible binding for global variable ‘refEnd’
orthologScale: no visible binding for global variable ‘refStart’
orthologScale: no visible binding for global variable ‘compareEnd’
orthologScale: no visible binding for global variable ‘compareStart’
orthologScale: no visible binding for global variable ‘.’
orthologScale: no visible binding for global variable
‘orthologyConfidence’
Undefined global functions or variables:
. compareEnd compareStart geneName group orthologyConfidence padj
pvalue refEnd refStart sepc teName
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'DECorrInputs.Rd':
\usage lines wider than 90 characters:
DECorrInputs(orthologTable, scaleFactor, geneCountRef, geneCountCompare, teCountRef, teCountCompare)
These lines will be truncated in the PDF manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [63s/63s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DEgeneTE 27.770 0.392 28.162
appTEKRABber 26.271 0.199 26.473
* 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: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2446/TEKRABber_20220113185942/TEKRABber.Rcheck/00check.log’
for details.
===============================
BiocCheck('TEKRABber_0.99.0.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...
* NOTE: Consider clarifying how 12 object(s) are initialized. Maybe
they are part of a data set loaded with data(), or perhaps part
of an object referenced in with() or within().
function (object)
appTEKRABber (group)
appTEKRABber (geneName)
appTEKRABber (teName)
appTEKRABber (padj)
assay_tekcorrset (sepc)
corrOrthologTE (pvalue)
orthologScale (refEnd)
orthologScale (refStart)
orthologScale (compareEnd)
orthologScale (compareStart)
orthologScale (.)
orthologScale (orthologyConfidence)
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 4.0 to 4.2.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
GeneExpression
See http://bioconductor.org/developers/how-to/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...
* NOTE: License 'GPL (>= 2)' unknown; licenses cannot restrict use
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/TEKRABber.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of TEKRABber...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
corrOrthologTE.R (line 33, column 23)
corrOrthologTE.R (line 36, column 28)
DECorrInputs.R (line 81, column 43)
DECorrInputs.R (line 83, column 39)
orthologScale.R (line 97, column 55)
* 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:
appTEKRABber() (R/appTEKRABber.R, line 59): 214 lines
server() (R/appTEKRABber.R, line 141): 129 lines
DEgeneTE() (R/DEgeneTE.R, line 34): 90 lines
orthologScale() (R/orthologScale.R, line 22): 84 lines
DECorrInputs() (R/DECorrInputs.R, line 35): 62 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
rcpp_corr.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
8% of man pages use one of these cases.
Found in the following files:
TEKRABber-package.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
TEKRABber-package.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 shorter lines; 143 lines (10%) are > 80 characters
long.
First 6 lines:
R/appTEKRABber.R:2 #' @description To help user explore their results u...
R/appTEKRABber.R:3 #' using a self-written shiny app with two tabs, inc...
R/appTEKRABber.R:7 #' @param corrRef the correlation result of your ref...
R/appTEKRABber.R:8 #' @param corrCompare the correlation result of your...
R/appTEKRABber.R:10 #' @return an app can display differentially expres...
R/appTEKRABber.R:19 #' metaExp$experiment <- factor(metaExp$experiment,...
* NOTE: Consider multiples of 4 spaces for line indents, 66
lines(5%) are not.
First 6 lines:
man/appTEKRABber.Rd:36 geneTable = geneInputDE,
man/appTEKRABber.Rd:37 teTable = teInputDE,
man/appTEKRABber.Rd:38 metadata = metaExp,
man/appTEKRABber.Rd:39 contrastVector = c("experiment", "control", "t...
man/appTEKRABber.Rd:40 expDesign = FALSE
man/assay_tekcorrset.Rd:16 are for running same species design.}
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
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* Checking if new package already exists in Bioconductor...
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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: 15
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nebbiolo1 BUILD BIN output
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