Bioconductor Single Package Builder - Build History
lconway Summary
| Package: HiBED |
| Version: 0.99.11 |
| RVersion: 4.3 |
| BiocVersion: 3.18 |
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data HiBED |
| BuildTime: 0 minutes 50.95 seconds |
| CheckCommand: BiocCheckGitClone('HiBED') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2965/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2965/c4200284645e55cd331ae54b7fe378b943b0919f/HiBED.install-out.txt HiBED_0.99.11.tar.gz && BiocCheck('HiBED_0.99.11.tar.gz', `new-package`=TRUE) |
| CheckTime: 4 minutes 16.29 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh HiBED_0.99.11.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 29.92 seconds |
| PackageFileSize: 40.43 KiB |
| BuildID:: HiBED_20230526132513 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: HiBED. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. Build Package status: 0. |
lconway BUILD SRC output
===============================
R CMD BUILD
===============================
* checking for file ‘HiBED/DESCRIPTION’ ... OK
* preparing ‘HiBED’:
* 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
* looking to see if a ‘data/datalist’ file should be added
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘HiBED/data/HiBED_Libraries.rda’
* building ‘HiBED_0.99.11.tar.gz’
lconway CHECK output
===============================
BiocCheckGitClone('HiBED')
===============================
─ BiocCheckVersion: 1.37.0
─ BiocVersion: 3.18
─ Package: HiBED
─ PackageVersion: 0.99.11
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2965/c4200284645e55cd331ae54b7fe378b943b0919f/HiBED
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2965/c4200284645e55cd331ae54b7fe378b943b0919f/HiBED.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84266)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiBED/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiBED’ version ‘0.99.11’
* 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 ‘HiBED’ can be installed ... 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] 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 ... [30s/30s] NOTE
HiBED_deconvolution: no visible global function definition for ‘data’
HiBED_deconvolution: no visible binding for global variable ‘Sum’
Undefined global functions or variables:
Sum data
Consider adding
importFrom("utils", "data")
to your NAMESPACE file.
* 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 ... [4s/4s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [22s/22s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
HiBED_deconvolution 9.76 0.648 10.408
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [19s/19s]
[19s/20s] 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 ... [4s/4s] OK
* DONE
Status: 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2965/c4200284645e55cd331ae54b7fe378b943b0919f/HiBED.Rcheck/00check.log’
for details.
===============================
BiocCheck('HiBED_0.99.11.tar.gz')
===============================
─ BiocCheckVersion: 1.37.0
─ BiocVersion: 3.18
─ Package: HiBED
─ PackageVersion: 0.99.11
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpKbjhsS/filec7341bedac03/HiBED
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpKbjhsS/filec73421e6108b
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2965/c4200284645e55cd331ae54b7fe378b943b0919f/HiBED.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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 4.3.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
ExperimentData
* 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...
* 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...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of HiBED...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
is 1 function greater than 50 lines.
* Checking man page documentation...
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
* 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; 2 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 99 lines
(23%) are not.
See https://contributions.bioconductor.org/r-code.html
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.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 5 NOTES
See the HiBED.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
lconway BUILD BIN output
=============================== R CMD BUILD =============================== >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir HiBED_0.99.11.tar.gz' >>>>>>> * installing *source* package ‘HiBED’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (HiBED)
nebbiolo2 Summary
| Package: HiBED |
| Version: 0.99.11 |
| RVersion: 4.3 |
| BiocVersion: 3.18 |
| BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data HiBED |
| BuildTime: 1 minutes 8.83 seconds |
| CheckCommand: BiocCheckGitClone('HiBED') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2965/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2965/c4200284645e55cd331ae54b7fe378b943b0919f/HiBED.install-out.txt HiBED_0.99.11.tar.gz && BiocCheck('HiBED_0.99.11.tar.gz', `new-package`=TRUE) |
| CheckTime: 5 minutes 16.96 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 40.59 KiB |
| BuildID:: HiBED_20230526132513 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: HiBED. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: ExperimentData. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
nebbiolo2 BUILD SRC output
===============================
R CMD BUILD
===============================
* checking for file ‘HiBED/DESCRIPTION’ ... OK
* preparing ‘HiBED’:
* 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
* looking to see if a ‘data/datalist’ file should be added
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘HiBED/data/HiBED_Libraries.rda’
* building ‘HiBED_0.99.11.tar.gz’
nebbiolo2 CHECK output
===============================
BiocCheckGitClone('HiBED')
===============================
─ BiocCheckVersion: 1.37.0
─ BiocVersion: 3.18
─ Package: HiBED
─ PackageVersion: 0.99.11
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2965/c4200284645e55cd331ae54b7fe378b943b0919f/HiBED
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2965/c4200284645e55cd331ae54b7fe378b943b0919f/HiBED.Rcheck’
* using R version 4.3.0 RC (2023-04-18 r84287)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiBED/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiBED’ version ‘0.99.11’
* 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 ‘HiBED’ can be installed ... 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 ... [13s/13s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/13s] OK
* checking loading without being on the library search path ... [13s/13s] 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 ... [41s/41s] NOTE
HiBED_deconvolution: no visible global function definition for ‘data’
HiBED_deconvolution: no visible binding for global variable ‘Sum’
Undefined global functions or variables:
Sum data
Consider adding
importFrom("utils", "data")
to your NAMESPACE file.
* 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 ... [6s/6s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [22s/22s] ERROR
Running examples in ‘HiBED-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HiBED_deconvolution
> ### Title: HiBED_deconvolution
> ### Aliases: HiBED_deconvolution
>
> ### ** Examples
>
> #Step 1: Load required libraries
> library(FlowSorted.Blood.EPIC)
Loading required package: minfi
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: ‘MatrixGenerics’
The following objects are masked from ‘package:matrixStats’:
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: ‘Biobase’
The following object is masked from ‘package:MatrixGenerics’:
rowMedians
The following objects are masked from ‘package:matrixStats’:
anyMissing, rowMedians
Loading required package: Biostrings
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: locfit
locfit 1.5-9.7 2023-01-02
Loading required package: ExperimentHub
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Attaching package: ‘AnnotationHub’
The following object is masked from ‘package:Biobase’:
cache
> library(FlowSorted.DLPFC.450k)
> #Step 2: Load example data and preprocess
> Mset<-minfi::preprocessRaw(FlowSorted.DLPFC.450k)
Loading required package: IlluminaHumanMethylation450kmanifest
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘IlluminaHumanMethylation450kmanifest’
Error in getManifest(object) :
cannot load manifest package IlluminaHumanMethylation450kmanifest
Calls: <Anonymous> ... getManifestInfo -> getProbeInfo -> getManifest -> getManifest
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [20s/20s]
[21s/21s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
> library(testthat)
> library(HiBED)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
>
> test_check("HiBED")
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 1 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test.R:8:3'): errors if bad parameters ──────────────────────────────
Error in `getManifest(object)`: cannot load manifest package IlluminaHumanMethylation450kmanifest
Backtrace:
▆
1. └─minfi::preprocessRaw(FlowSorted.DLPFC.450k) at test.R:8:2
2. └─minfi::getManifestInfo(rgSet, "locusNames")
3. └─minfi::getProbeInfo(object, type = "I")
4. ├─minfi::getManifest(object)
5. └─minfi::getManifest(object)
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 1 ]
Error: Test failures
Execution halted
* 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 ... [2s/2s] OK
* DONE
Status: 2 ERRORs, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2965/c4200284645e55cd331ae54b7fe378b943b0919f/HiBED.Rcheck/00check.log’
for details.
===============================
BiocCheck('HiBED_0.99.11.tar.gz')
===============================
─ BiocCheckVersion: 1.37.0
─ BiocVersion: 3.18
─ Package: HiBED
─ PackageVersion: 0.99.11
─ sourceDir: /tmp/RtmpsSxPEm/file2dd6b5349e6209/HiBED
─ installDir: /tmp/RtmpsSxPEm/file2dd6b511acb5d4
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2965/c4200284645e55cd331ae54b7fe378b943b0919f/HiBED.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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 4.3.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
ExperimentData
* 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...
* 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...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of HiBED...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
is 1 function greater than 50 lines.
* Checking man page documentation...
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
* 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; 2 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 99 lines
(23%) are not.
See https://contributions.bioconductor.org/r-code.html
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.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 5 NOTES
See the HiBED.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.