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BiocCheckGitClone('scDDboost')
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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...
* 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/3.14/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/2349/b49cc3ab23d60cdaafc8b57b2b6683547e7b1bf4/scDDboost.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 ‘scDDboost/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scDDboost’ version ‘0.99.4’
* checking package namespace information ... NOTE
Namespace with empty importFrom: ‘stats’
* 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 ‘scDDboost’ can be installed ... [64s/65s] OK
* checking installed package size ... NOTE
installed size is 14.6Mb
sub-directories of 1Mb or more:
libs 14.1Mb
* 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 ... [21s/21s] NOTE
extractInfo: no visible global function definition for ‘is’
Undefined global functions or variables:
is
Consider adding
importFrom("methods", "is")
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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File ‘scDDboost/libs/scDDboost.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [97s/38s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PDD 19.392 2.398 8.976
scDDboost-package 19.064 2.167 7.484
cal_D 16.660 2.172 5.033
detK 15.847 2.100 4.676
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘ggplot2’
* 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: 5 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2349/b49cc3ab23d60cdaafc8b57b2b6683547e7b1bf4/scDDboost.Rcheck/00check.log’
for details.
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BiocCheck('scDDboost_0.99.4.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 1 object(s) are initialized. Maybe
it is part of a data set loaded with data(), or perhaps part of
an object referenced in with() or within().
function (object)
extractInfo (is)
* 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...
* NOTE: Consider adding these automatically suggested biocViews:
DifferentialExpression, Bayesian
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...
* NOTE: License 'GPL (>= 2)' unknown; licenses cannot restrict use
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/scDDboost.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of scDDboost...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
PDD.R (line 37, column 17)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
g_cl.R (line 25, column 21)
g_cl.R (line 27, column 14)
listsize.R (line 19, column 23)
lsz.R (line 23, column 23)
MDD.R (line 65, column 15)
PDD_random.R (line 26, column 11)
PDD_random.R (line 28, column 11)
PDD_random.R (line 29, column 11)
PDD_random.R (line 30, column 14)
PDD.R (line 37, column 24)
PDD.R (line 47, column 11)
PDD.R (line 125, column 18)
PDD.R (line 169, column 27)
PDD.R (line 173, column 18)
rwMLE.R (line 15, column 14)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
/tmp/Rtmp7BtaN0/file393bd131fe9464/scDDboost/R/PDD.R (line 41,
column 13)
/tmp/Rtmp7BtaN0/file393bd131fe9464/scDDboost/R/PDD.R (line 85,
column 21)
/tmp/Rtmp7BtaN0/file393bd131fe9464/scDDboost/R/PDD.R (line 153,
column 17)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
suppressWarnings() in R/rwMLE.R (line 21, column 13)
* Checking function lengths.............................
* NOTE: Recommended function length <= 50 lines.
There are 1 functions > 50 lines.
The longest 5 functions are:
PDD() (R/PDD.R, line 30): 157 lines
PDD_random() (R/PDD_random.R, line 20): 43 lines
cal_D() (R/cal_D.R, line 17): 39 lines
detK() (R/detK.R, line 15): 27 lines
g_cl() (R/g_cl.R, line 8): 25 lines
* Checking man page documentation...
* 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; 57 lines (4%) are > 80 characters
long.
First 6 lines:
R/EBS.R:11 #' @param stp1 step size of hyperparameter alpha (shared by ...
R/EBS.R:36 .Call('EBS', X=data,Y=conditions,Z=gclus,W=sf, iter=iter...
R/g_cl.R:21 message("estimation of hyper parameter failed, try nai...
R/g_cl.R:25 clus = bplapply(1:nr,function(i) MCP(data[i,],1,c(Phi_m...
R/g_ref.R:4 #' @return return a matrix indicate the refinement relation...
R/LL.R:25 res = (n - nc) * (lgamma(a0 + a1) - lgamma(a0) - lgamma(a...
* NOTE: Consider multiples of 4 spaces for line indents, 45
lines(3%) are not.
First 6 lines:
R/cal_D.R:41
R/detK.R:17 intra = rep(0,8)
R/detK.R:18 inter = rep(0,8)
R/detK.R:20 for(i in 2:9){
R/detK.R:21 clusRes = pam(D,i,diss = TRUE)
R/detK.R:22 intra[i - 1] = as.numeric(clusRes$objective[1])
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.
* 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: 1
WARNING count: 0
NOTE count: 13
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.