===============================
BiocCheckGitClone('SC.MEB')
===============================
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:
SC.MEB.Rproj
.Rhistory
src-i386/bkRcpp.o
src-i386/RcppExports.o
src-x64/bkRcpp.o
src-x64/RcppExports.o
src-i386/SC.MEB.so
src-x64/SC.MEB.so
src/SC.MEB.so
src-i386/SC.MEB.dll
src-x64/SC.MEB.dll
src/SC.MEB.dll
.DS_Store
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* 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.
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2245/SC.MEB_20210901152546/SC.MEB.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 ‘SC.MEB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SC.MEB’ 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 ‘SC.MEB’ can be installed ... [20s/20s] OK
* checking installed package size ... NOTE
installed size is 7.0Mb
sub-directories of 1Mb or more:
libs 6.2Mb
* checking package directory ... OK
* checking for future file timestamps ... 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 ... WARNING
'library' or 'require' calls not declared from:
‘Matrix’ ‘ggplot2’ ‘parallel’ ‘purrr’
'library' or 'require' call to ‘mclust’ which was already attached by Depends.
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘Matrix’ ‘ggplot2’ ‘parallel’ ‘purrr’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
‘Matrix’ ‘SingleCellExperiment’ ‘purrr’
All declared Imports should be used.
Package in Depends field not imported from: ‘mclust’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [2s/2s] NOTE
ClusterPlot: no visible global function definition for ‘ggplot’
ClusterPlot: no visible global function definition for ‘aes’
ClusterPlot: no visible binding for global variable ‘cluster’
ClusterPlot: no visible global function definition for ‘geom_point’
ClusterPlot: no visible global function definition for ‘theme’
ClusterPlot: no visible global function definition for ‘element_blank’
ClusterPlot: no visible global function definition for ‘unit’
ClusterPlot: no visible global function definition for ‘element_text’
SC.MEB: no visible global function definition for ‘makeCluster’
SC.MEB: no visible global function definition for ‘clusterExport’
SC.MEB: no visible global function definition for ‘parSapply’
SC.MEB: no visible global function definition for ‘stopCluster’
SC.MEB: no visible binding for global variable ‘Adj’
find_neighbors2: no visible global function definition for ‘colData’
find_neighbors2: no visible global function definition for ‘map’
find_neighbors2 : <anonymous>: no visible global function definition
for ‘discard’
find_neighbors2: no visible global function definition for ‘keep’
find_neighbors2: no visible global function definition for
‘sparseMatrix’
parafun: no visible global function definition for ‘Mclust’
selectK: no visible binding for global variable ‘fit’
selectKPlot: no visible binding for global variable ‘fit’
selectKPlot: no visible global function definition for ‘ggplot’
selectKPlot: no visible global function definition for ‘aes’
selectKPlot: no visible global function definition for ‘geom_line’
selectKPlot: no visible global function definition for ‘geom_point’
spatialPreprocess: no visible global function definition for
‘ExactParam’
spatialPreprocess: no visible global function definition for ‘metadata’
spatialPreprocess: no visible global function definition for
‘metadata<-’
spatialPreprocess: no visible global function definition for
‘logNormCounts’
spatialPreprocess: no visible global function definition for
‘modelGeneVar’
spatialPreprocess: no visible global function definition for
‘getTopHVGs’
spatialPreprocess: no visible global function definition for ‘runPCA’
spatialPreprocess: no visible global function definition for ‘rowData’
spatialPreprocess: no visible global function definition for
‘rowData<-’
Undefined global functions or variables:
Adj ExactParam Mclust aes cluster clusterExport colData discard
element_blank element_text fit geom_line geom_point getTopHVGs ggplot
keep logNormCounts makeCluster map metadata metadata<- modelGeneVar
parSapply rowData rowData<- runPCA sparseMatrix stopCluster theme
unit
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'spatialPreprocess.Rd':
‘BiocSingularParam-class’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'SC.MEB'
‘...’
Undocumented arguments in documentation object 'parafun'
‘Adj’
Documented arguments not in \usage in documentation object 'parafun':
‘Adj_sp’
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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File ‘SC.MEB/libs/SC.MEB.so’:
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Object: ‘bkRcpp.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
‘SC.MEB.Rmd’, ‘SC.MEB_CRC.Rmd’, ‘SC.MEB_CRC.html’
Files named as vignettes but with no recognized vignette engine:
‘vignettes/SC.MEB.Rmd’
‘vignettes/SC.MEB_CRC.Rmd’
(Is a VignetteBuilder field missing?)
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE
Status: 4 WARNINGs, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2245/SC.MEB_20210901152546/SC.MEB.Rcheck/00check.log’
for details.
===============================
BiocCheck('SC.MEB_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...
* ERROR: Packages providing 7 object(s) used in this package should
be imported in the NAMESPACE file, otherwise packages importing
this package may fail.
package::object in function()
SingleCellExperiment::colData in find_neighbors2()
purrr::map in find_neighbors2()
purrr::discard in find_neighbors2 ()
purrr::keep in find_neighbors2()
Matrix::sparseMatrix in find_neighbors2()
mclust::Mclust in parafun()
SingleCellExperiment::rowData in spatialPreprocess()
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 27 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)
ClusterPlot (ggplot)
ClusterPlot (aes)
ClusterPlot (cluster)
ClusterPlot (geom_point)
ClusterPlot (theme)
ClusterPlot (element_blank)
ClusterPlot (unit)
ClusterPlot (element_text)
SC.MEB (makeCluster)
SC.MEB (clusterExport)
SC.MEB (parSapply)
SC.MEB (stopCluster)
SC.MEB (Adj)
selectK (fit)
selectKPlot (fit)
selectKPlot (ggplot)
selectKPlot (aes)
selectKPlot (geom_line)
selectKPlot (geom_point)
spatialPreprocess (ExactParam)
spatialPreprocess (metadata)
spatialPreprocess (metadata<-)
spatialPreprocess (logNormCounts)
spatialPreprocess (modelGeneVar)
spatialPreprocess (getTopHVGs)
spatialPreprocess (runPCA)
spatialPreprocess (rowData<-)
* 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 3.5.0 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...
* NOTE: Consider adding these automatically suggested biocViews:
Spatial
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...
* 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 DESCRIPTION/NAMESPACE consistency...
* WARNING: Import SingleCellExperiment, purrr, Matrix in NAMESPACE
as well as DESCRIPTION.
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: Potential intermediate files found:
vignettes/sc.meb_crc.html
* ERROR: VignetteBuilder listed in DESCRIPTION but not found as
VignetteEngine in any vignettes:
knitr
* ERROR: VignetteEngine specified but not in DESCRIPTION. Add the
VignetteEngine from the following files to DESCRIPTION:
SC.MEB_CRC.Rmd
SC.MEB.Rmd
* WARNING: Package listed as VignetteEngine or VignetteBuilder but
not currently Suggested. Add the following to Suggests in
DESCRIPTION:
UTF-8
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/SC.MEB_CRC.Rmd
vignettes/SC.MEB.Rmd
* Checking whether vignette is built with 'R CMD build'...
* ERROR: Vignette must be built by 'R CMD build'. Please see the
`Vignette Checks` section of the BiocCheck vignette.
* Checking package installation calls in R code...
* Checking for library/require of SC.MEB...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
find_neighbours.R (line 66, column 25)
find_neighbours.R (line 66, column 34)
find_neighbours.R (line 67, column 13)
SC-MEB.R (line 25, column 15)
SC-MEB.R (line 38, column 15)
SC-MEB.R (line 117, column 15)
SC-MEB.R (line 129, column 15)
SC-MEB.R (line 186, column 15)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths......
* NOTE: Recommended function length <= 50 lines.
There are 1 functions > 50 lines.
The longest 5 functions are:
find_neighbors2() (R/find_neighbours.R, line 12): 61 lines
selectK() (R/SC-MEB.R, line 15): 35 lines
selectKPlot() (R/SC-MEB.R, line 110): 31 lines
ClusterPlot() (R/SC-MEB.R, line 64): 26 lines
spatialPreprocess() (R/spatialProcess.R, line 35): 26 lines
* Checking man page documentation...
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples. The following pages do not:
ClusterPlot.Rd, find_neighbors2.Rd, getneighborhood_fast.Rd,
ICMEM.Rd, parafun.Rd, SC.MEB.Rd, selectK.Rd, selectKPlot.Rd,
spatialPreprocess.Rd
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 107 lines (10%) are > 80 characters
long.
First 6 lines:
R/find_neighbours.R:8 #' @param sce is a SingleCellExperiment object co...
R/find_neighbours.R:9 #' @param platform is the name of spatial transcr...
R/find_neighbours.R:33 neighbor.positions$x.pos <- neighbor.positions...
R/find_neighbours.R:34 neighbor.positions$y.pos <- neighbor.positions...
R/RcppExports.R:7 #' an efficient function to find the neighborhood bas...
R/RcppExports.R:10 #' @param cutoff is a threashold of Euclidean distan...
* NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain
tabs.
First 1 lines:
vignettes/SC.MEB.Rmd:61 for(i in 1:n) { # cell
* NOTE: Consider multiples of 4 spaces for line indents, 206
lines(20%) are not.
First 6 lines:
R/find_neighbours.R:13 library(purrr)
R/find_neighbours.R:14 library(Matrix)
R/find_neighbours.R:15 if (platform == "Visium") {
R/find_neighbours.R:18 y.offset=c( 0, 0, -1, ...
R/find_neighbours.R:19 } else if (platform == "ST") {
R/find_neighbours.R:22 y.offset=c(-1, 0, 1, 0))
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...
* ERROR: Maintainer must register at the support site; visit
https://support.bioconductor.org/accounts/signup/ .
Summary:
ERROR count: 7
WARNING count: 2
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.