===============================
R CMD BUILD
===============================
* checking for file ‘CompoundDb/DESCRIPTION’ ... OK
* preparing ‘CompoundDb’:
* 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 ‘CompoundDb_0.99.0.tar.gz’
===============================
BiocCheckGitClone('CompoundDb')
===============================
This is BiocCheckGitClone version 1.31.21. 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/2466/CompoundDb_20220106183653/CompoundDb.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 ‘CompoundDb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CompoundDb’ version ‘0.99.0’
* 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 serialization versions ... OK
* checking whether package ‘CompoundDb’ 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 ... 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 ... [13s/13s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [8s/8s]
[8s/8s] 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 ... OK
* DONE
Status: OK
===============================
BiocCheck('CompoundDb_0.99.0.tar.gz')
===============================
This is BiocCheck version 1.31.21. 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...
* NOTE: Update R version dependency from 3.4 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...
* 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 vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of CompoundDb...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
times)
suppressWarnings() in R/createCompDbPackage.R (line 87, column
5)
suppressMessages() in R/createCompDbPackage.R (line 1042,
column 5)
suppressWarnings() in R/IonDb.R (line 265, column 5)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 2 functions > 50 lines.
The longest 5 functions are:
.import_hmdb_ms_ms_spectrum() (R/spectrum-import-functions.R,
line 42): 67 lines
createCompDb() (R/createCompDbPackage.R, line 561): 59 lines
.validCompDb() (R/CompDb.R, line 256): 49 lines
_anonymous_.128() (R/CompDb-methods.R, line 128): 43 lines
.simple_extract_compounds_sdf() (R/createCompDbPackage.R, line
179): 43 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
MsBackendCompDb.Rd
* Checking package NEWS...
* 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; 159 lines (3%) are > 80 characters
long.
First 6 lines:
man/CompDb.Rd:38 \S4method{Spectra}{CompDb}(object, columns = spectraVa...
man/CompDb.Rd:56 \S4method{insertSpectra}{CompDb,Spectra}(object, spect...
man/CompDb.Rd:63 to the database with parameter \code{x}. For \code{cop...
man/CompDb.Rd:68 See \code{\link[=SQLite]{SQLite()}}. Defaults to read-...
man/CompDb.Rd:75 \item{columns}{For \code{compounds}, \code{Spectra}: \...
man/CompDb.Rd:82 \code{\link[=AnnotationFilter]{AnnotationFilter()}} de...
* NOTE: Consider multiples of 4 spaces for line indents, 508
lines(8%) are not.
First 6 lines:
R/AllGenerics.R:8 standardGeneric("ionVariables"))
R/AllGenerics.R:11 standardGeneric("insertIon"))
R/AllGenerics.R:14 standardGeneric("insertSpectra"))
R/AllGenerics.R:17 standardGeneric("deleteIon"))
R/AllGenerics.R:20 standardGeneric("deleteSpectra"))
R/AllGenerics.R:31 c("numeric", "DataFrameOrEquivalent"))
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: 6
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