===============================
BiocCheckGitClone('TSSr')
===============================
This is BiocCheckGitClone version 1.29.14. 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...
* Checking that provided CITATION file is correctly formatted...
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/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
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R CMD CHECK
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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2222/43956753c8d55096a125376a7c2fda43fa6e0243/TSSr.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TSSr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TSSr’ version ‘0.99.5’
* 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 ‘TSSr’ can be installed ... [32s/32s] 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 ... [33s/33s] 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 data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [99s/96s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
consensusCluster 53.683 0.353 52.852
annotateCluster 5.153 0.379 5.380
* 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
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BiocCheck('TSSr_0.99.5.tar.gz')
===============================
This is BiocCheck version 1.29.14. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* Checking package size...
* 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...
* NOTE: License 'file LICENSE' unknown; licenses cannot restrict
use
* 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 TSSr...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
ClusteringFunctions.R (line 28, column 15)
ClusteringFunctions.R (line 33, column 15)
ConsensusMethods.R (line 54, column 18)
EnhancerMethods.R (line 84, column 20)
ExpressionFunctions.R (line 74, column 24)
ExpressionFunctions.R (line 75, column 24)
ExpressionFunctions.R (line 115, column 15)
ExpressionFunctions.R (line 124, column 15)
ExpressionFunctions.R (line 150, column 15)
ExpressionFunctions.R (line 159, column 15)
ExpressionMethods.R (line 55, column 14)
ImportFunctions.R (line 45, column 38)
ShapeMethods.R (line 63, column 36)
ShapeMethods.R (line 65, column 37)
ShapeMethods.R (line 85, column 36)
ShapeMethods.R (line 87, column 37)
ShiftingMethods.R (line 45, column 14)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
times)
suppressWarnings() in R/AnnotationMethods.R (line 70, column
13)
suppressWarnings() in R/ExportFunctions.R (line 21, column 3)
suppressWarnings() in R/ShiftingFunctions.R (line 48, column
15)
* Checking function lengths.................................................
* NOTE: Recommended function length <= 50 lines.
There are 14 functions > 50 lines.
The longest 5 functions are:
.assign2gene() (R/AnnotationFunctions.R, line 3): 112 lines
.clusterByPeak() (R/ClusteringFunctions.R, line 3): 110 lines
.getTSS_from_bam() (R/ImportFunctions.R, line 13): 107 lines
_anonymous_.10() (R/AnnotationFunctions.R, line 10): 102 lines
_anonymous_.47() (R/AnnotationMethods.R, line 47): 94 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
callEnhancer.Rd, clusterTSS.Rd, getTSS.Rd, shapeCluster.Rd,
shiftPromoter.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
18% of man pages use one of these cases.
Found in the following files:
callEnhancer.Rd
clusterTSS.Rd
getTSS.Rd
shapeCluster.Rd
shiftPromoter.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; 437 lines (11%) are > 80 characters
long.
First 6 lines:
R/Aclasses.R:3 #' TSSr is designed to analyze transcription start sites...
R/Aclasses.R:4 #' with most types of 5’end sequencing data, such as cap...
R/Aclasses.R:5 #' (Takahashi, Lassmann et al. 2012), no-amplification n...
R/Aclasses.R:6 #' Illumina next-generation sequencers (nAnT-iCAGE) (Mur...
R/Aclasses.R:8 #' NanoCAGE (Cumbie, Ivanchenko et al. 2015), TSS-seq (M...
R/Aclasses.R:14 #' TSSr package provides a comprehensive workflow on TS...
* NOTE: Consider multiples of 4 spaces for line indents, 1205
lines(30%) are not.
First 6 lines:
R/Aclasses.R:89 representation(genomeName = "character"
R/Aclasses.R:111 ),
R/Aclasses.R:112 prototype(genomeName = character()
R/Aclasses.R:113 ,inputFiles = character()
R/Aclasses.R:114 ,inputFilesType = character()
R/Aclasses.R:115 ,sampleLabels = character()
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/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output