===============================
BiocCheckGitClone('mbOmic')
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This is BiocCheckGitClone version 1.29.14. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
mbOmic.Rproj
* 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: 2
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
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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2234/mbOmic_20210824184405/mbOmic.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 ‘mbOmic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mbOmic’ 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 ‘mbOmic’ can be installed ... [13s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
package 'methods' is used but not declared
* checking S3 generic/method consistency ... WARNING
print:
function(x, ...)
print.mbSet:
function(obj)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [12s/12s] NOTE
b.extra: no visible binding for global variable ‘..s’
m.extra: no visible binding for global variable ‘..s’
m.filter: no visible binding for global variable ‘..goodMetabolites’
mbSet: no visible binding for global variable ‘..m.id’
mbSet: no visible binding for global variable ‘..b.id’
mbSet: no visible global function definition for ‘new’
pickST: no visible global function definition for ‘capture.output’
pickST: no visible global function definition for ‘points’
pickST: no visible global function definition for ‘text’
pickST: no visible global function definition for ‘abline’
plot_network: no visible binding for global variable ‘name’
plot_network: no visible binding for global variable ‘centrality
degree’
plot_network: no visible global function definition for ‘quantile’
plot_network: no visible binding for global variable ‘label’
clean_analytes,mbSet: no visible binding for global variable
‘..samples’
corr,mbSet: no visible global function definition for ‘stopCluster’
corr,mbSet : <anonymous>: no visible global function definition for
‘setNames’
corr,mbSet: no visible binding for global variable ‘.’
corr,mbSet: no visible global function definition for ‘.’
corr,mbSet: no visible binding for global variable ‘rho’
corr,mbSet: no visible binding for global variable ‘p’
corr,mbSet: no visible binding for global variable ‘padj’
wgcna,mbSet: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
. ..b.id ..goodMetabolites ..m.id ..s ..samples abline capture.output
centrality degree label name new p padj points quantile rho setNames
stopCluster text
Consider adding
importFrom("graphics", "abline", "points", "text")
importFrom("methods", "new")
importFrom("stats", "quantile", "setNames")
importFrom("utils", "capture.output")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... WARNING
Undocumented data sets:
‘genera’ ‘metabolites’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'check_mbSet'
‘object’
Undocumented arguments in documentation object 'cor2df'
‘res’
Undocumented arguments in documentation object 'corr'
‘...’
Undocumented arguments in documentation object 'm.filter'
‘m’ ‘minNSamples’
Undocumented arguments in documentation object 'mbSet'
‘pData’
Undocumented arguments in documentation object 'pickST'
‘m’ ‘threshold.d’ ‘threshold’ ‘plot’ ‘powers’
Assignments in \usage in documentation object 'plot_network':
threshold = 0.9
Undocumented arguments in documentation object 'plot_wgcna'
‘net’ ‘...’
Undocumented arguments in documentation object 'show,mbSet-method'
‘object’
Undocumented arguments in documentation object 'wgcna,mbSet-method'
‘object’ ‘group’ ‘minN’ ‘power’ ‘powers’ ‘threshold.d’ ‘threshold’
‘message’ ‘...’
Undocumented arguments in documentation object 'wgcna'
‘group’ ‘powers’ ‘threshold.d’ ‘threshold’ ‘message’ ‘...’
Bad \usage lines found in documentation object 'plot_network':
plot_network(
net = net,
corr = corr,
centrality_degree_mode = 'out',
)
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
Note: found 11 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [16s/16s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
wgcna 5.817 0 5.818
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [5s/4s]
[5s/5s] 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:
! Package inputenc Error: Unicode character , (U+FF0C)
(inputenc) not set up for use with LaTeX.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
* checking PDF version of manual without hyperrefs or index ... ERROR
* DONE
Status: 1 ERROR, 4 WARNINGs, 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2234/mbOmic_20210824184405/mbOmic.Rcheck/00check.log’
for details.
===============================
BiocCheck('mbOmic_0.99.1.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...
* NOTE: Consider clarifying how 14 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)
b.extra (..s)
m.extra (..s)
m.filter (..goodMetabolites)
mbSet (..m.id)
mbSet (..b.id)
mbSet (new)
pickST (capture.output)
pickST (points)
pickST (text)
pickST (abline)
plot_network (name)
plot_network (centrality degree)
plot_network (quantile)
plot_network (label)
* 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 to 4.1.0.
* 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...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* WARNING: Description field in the DESCRIPTION file is too concise
* 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...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/Integrative_analysis_of_metabolome_and_microbiome.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of mbOmic...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
methods.R (line 110, column 34)
methods.R (line 114, column 34)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
functions.R (line 195, column 53)
methods.R (line 147, column 74)
methods.R (line 158, column 80)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
suppressMessages() in R/functions.R (line 172, column 17)
* Checking function lengths.................
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
plot_network.Rd, plot_wgcna.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
11% of man pages use one of these cases.
Found in the following files:
plot_network.Rd
plot_wgcna.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
plot_network.Rd
plot_wgcna.Rd
* 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; 46 lines (4%) are > 80 characters
long.
First 6 lines:
R/classes.R:12 msg <- "The names of m o...
R/functions.R:175 ...
R/functions.R:176 ...
R/functions.R:179 cat("\nRemoving metabo...
R/functions.R:181 paste(names(m)[!su...
R/functions.R:194 function(m, threshold.d = 0.05, threshold = 0...
* NOTE: Consider multiples of 4 spaces for line indents, 157
lines(13%) are not.
First 6 lines:
R/classes.R:30 b = 'data.t...
R/classes.R:31 pData = 'da...
R/classes.R:32 samples = "...
R/classes.R:33 nb = 'integ...
R/classes.R:34 nm = 'integ...
R/classes.R:35 ms = 'factor',
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: 3
WARNING count: 1
NOTE count: 12
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.