===============================
BiocCheckGitClone('LINEAGE')
===============================
This is BiocCheckGitClone version 1.29.16. 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...
* ERROR: Do not use Author/Maintainer fields. Use Authors@R.
* Checking CITATION...
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
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R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2393/LINEAGE_20211022172312/LINEAGE.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 ‘LINEAGE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LINEAGE’ version ‘0.99.1’
* 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 ‘LINEAGE’ can be installed ... [5s/5s] 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 ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [5s/5s] NOTE
data_prepare: no visible binding for global variable ‘altAllele’
data_prepare: no visible binding for global variable ‘refAllele’
main: no visible binding for global variable ‘tsne_1’
main: no visible binding for global variable ‘tsne_2’
main: no visible binding for global variable ‘tsne1’
main: no visible binding for global variable ‘tsne2’
main: no visible binding for global variable ‘group’
traceplot: no visible binding for global variable ‘tsne1’
traceplot: no visible binding for global variable ‘tsne2’
traceplot: no visible binding for global variable ‘umap1’
traceplot: no visible binding for global variable ‘umap2’
Undefined global functions or variables:
altAllele group refAllele tsne1 tsne2 tsne_1 tsne_2 umap1 umap2
* 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 ... ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('LINEAGE_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.29.16. 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 11 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)
data_prepare (altAllele)
data_prepare (refAllele)
main (tsne_1)
main (tsne_2)
main (tsne1)
main (tsne2)
main (group)
traceplot (tsne1)
traceplot (tsne2)
traceplot (umap1)
traceplot (umap2)
* 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...
* NOTE: Update R version dependency from 3.6.0 to 4.1.0.
* Checking package size...
* ERROR: Package Source tarball exceeds Bioconductor size
requirement.
Package Size: 7.8524 MB
Size Requirement: 5.0000 MB
* 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:
WholeGenome
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...
* ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive 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 LINEAGE...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
functions.R (line 129, column 16)
functions.R (line 130, column 16)
functions.R (line 217, column 10)
functions.R (line 332, column 14)
functions.R (line 343, column 14)
functions.R (line 358, column 14)
functions.R (line 368, column 14)
functions.R (line 377, column 53)
functions.R (line 397, column 25)
functions.R (line 402, column 7)
functions.R (line 414, column 29)
functions.R (line 415, column 20)
functions.R (line 429, column 59)
functions.R (line 454, column 26)
functions.R (line 455, column 26)
functions.R (line 459, column 14)
functions.R (line 460, column 18)
functions.R (line 468, column 52)
functions.R (line 470, column 29)
functions.R (line 517, column 22)
functions.R (line 544, column 34)
functions.R (line 545, column 26)
functions.R (line 548, column 34)
functions.R (line 549, column 26)
functions.R (line 553, column 14)
functions.R (line 625, column 28)
functions.R (line 626, column 22)
functions.R (line 641, column 34)
functions.R (line 642, column 26)
functions.R (line 645, column 34)
functions.R (line 646, column 26)
functions.R (line 650, column 14)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths........................
* NOTE: Recommended function length <= 50 lines.
There are 3 functions > 50 lines.
The longest 5 functions are:
main() (R/functions.R, line 328): 148 lines
multi_best_iter() (R/functions.R, line 601): 61 lines
best_iter() (R/functions.R, line 510): 55 lines
traceplot() (R/traceplot.R, line 32): 37 lines
data_prepare() (R/functions.R, line 29): 32 lines
* Checking man page documentation...
* 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; 123 lines (8%) are > 80 characters
long.
First 6 lines:
R/diss.R:4 #' @description A list containing Euclidean distance matrixe...
R/functions.R:15 #' @description Split the mitochondrial genotype matri...
R/functions.R:17 #' @param data A dataframe containing mitochondrial va...
R/functions.R:18 #' "altAllele" column represents the mutant allele; "r...
R/functions.R:25 #' @return A list containing 12 submatrices with diffe...
R/functions.R:67 #' @description Using mitochondrial variants frequency...
* NOTE: Consider multiples of 4 spaces for line indents, 5
lines(0%) are not.
First 5 lines:
man/multi_best_iter.Rd:8 d,
man/multi_best_iter.Rd:9 centers = c(2, 3),
man/multi_best_iter.Rd:10 nmarker = c(10, 15, 20),
man/multi_best_iter.Rd:11 repeats = 30,
man/multi_best_iter.Rd:12 thread = 10
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...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
Summary:
ERROR count: 4
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
BiocCheck FAILED.