nebbiolo1 Summary
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| Package: SUITOR |
| Version: 0.99.1 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SUITOR |
| BuildTime: 0 minutes 13.49 seconds |
| CheckCommand: BiocCheckGitClone('SUITOR') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings SUITOR_0.99.1.tar.gz && BiocCheck('SUITOR_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 34.88 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 312.84 KiB |
| BuildID:: SUITOR_20220309132327 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SUITOR. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘SUITOR/DESCRIPTION’ ... OK
* preparing ‘SUITOR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* 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
* building ‘SUITOR_0.99.1.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('SUITOR')
===============================
This is BiocCheckGitClone version 1.31.36. 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/2515/SUITOR_20220309132327/SUITOR.Rcheck’
* using R Under development (unstable) (2022-02-17 r81757)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SUITOR/DESCRIPTION’ ... OK
* this is package ‘SUITOR’ version ‘0.99.1’
* 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 ‘SUITOR’ can be installed ... [3s/3s] 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 ... [3s/3s] 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 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
suitor_extract_WH 6.761 0.024 6.785
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [1s/1s]
[1s/1s] 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('SUITOR_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.31.36. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2515/SUITOR_20220309132327/SUITOR_0.99.1.tar.gz" "/tmp/RtmpA0Mehe/file3499c76f39c467/lib" 2>/dev/null' had status 1
* 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 3.5.0 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...
* 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...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import stats, utils, graphics in DESCRIPTION as well as
NAMESPACE.
* 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 SUITOR...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
source_extract_WH.R (line 24, column 47)
source_extract_WH.R (line 28, column 47)
source_extract_WH.R (line 52, column 15)
source_extract_WH.R (line 73, column 13)
source_extract_WH.R (line 108, column 22)
source_extract_WH.R (line 112, column 22)
source.R (line 65, column 21)
source.R (line 67, column 24)
source.R (line 71, column 15)
source.R (line 119, column 13)
source.R (line 210, column 15)
source.R (line 232, column 22)
source.R (line 236, column 22)
source.R (line 262, column 13)
source.R (line 324, column 13)
source.R (line 329, column 15)
source.R (line 354, column 11)
source.R (line 432, column 13)
source.R (line 460, column 13)
source.R (line 465, column 13)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/source_extract_WH.R (line 84, column 14)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/source.R (line 74, column 29)
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/source.R (line 19, column 27)
R/source.R (line 20, column 54)
R/source.R (line 22, column 30)
R/source.R (line 23, column 31)
R/source.R (line 24, column 27)
R/source.R (line 25, column 35)
R/source.R (line 56, column 29)
R/source.R (line 57, column 29)
R/source.R (line 58, column 39)
R/source.R (line 59, column 45)
R/source.R (line 60, column 29)
R/source.R (line 61, column 29)
R/source.R (line 62, column 49)
R/source.R (line 68, column 24)
R/source.R (line 74, column 35)
R/source.R (line 91, column 56)
R/source.R (line 113, column 33)
R/source.R (line 129, column 39)
R/source.R (line 146, column 30)
R/source.R (line 157, column 30)
R/source.R (line 214, column 27)
R/source.R (line 414, column 22)
R/source.R (line 419, column 10)
R/source.R (line 423, column 39)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 2 functions > 50 lines.
The longest 5 functions are:
check_op() (R/source.R, line 24): 60 lines
getSummary() (R/source.R, line 260): 60 lines
default.list() (R/source.R, line 343): 49 lines
suitor_seq_C() (R/source.R, line 214): 46 lines
set_op_par() (R/source.R, line 84): 35 lines
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
12% of man pages use one of these cases.
Found in the following files:
suitor.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
suitor.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; 119 lines (10%) are > 80 characters
long.
First 6 lines:
R/source_extract_WH.R:44 clusterExport(cl=clus, c("extractWH_seq_...
R/source_extract_WH.R:112 ret <- foreach(i=1:n, .verbose=FALSE, .in...
R/source.R:20 if (!is.matrix(data) && !is.data.frame(data)) stop("ERR...
R/source.R:58 if (op$min.rank > op$max.rank) stop("ERROR with option ...
R/source.R:74 if (op$min.rank > m) stop(paste("ERROR: option min.rank...
R/source.R:178 tmp <- .C("C_call_nmf", as.numeric(x), as.integer(ia...
* NOTE: Consider multiples of 4 spaces for line indents, 437
lines(38%) are not.
First 6 lines:
R/source_extract_WH.R:3
R/source_extract_WH.R:4 data <- check_data(data)
R/source_extract_WH.R:5 nr <- nrow(data)
R/source_extract_WH.R:6 nc <- ncol(data)
R/source_extract_WH.R:7 if (!is.list(op)) op <- list()
R/source_extract_WH.R:8 op$min.rank <- rank
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: 2
NOTE count: 10
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
BiocCheck FAILED.
nebbiolo1 BUILD BIN output
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merida1 Summary
[top]
| Package: SUITOR |
| Version: 0.99.1 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SUITOR |
| BuildTime: 0 minutes 46.15 seconds |
| CheckCommand: BiocCheckGitClone('SUITOR') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SUITOR_0.99.1.tar.gz && BiocCheck('SUITOR_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 2 minutes 25.36 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh SUITOR_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 13.56 seconds |
| PackageFileSize: 421.57 KiB |
| BuildID:: SUITOR_20220309132327 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SUITOR. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘SUITOR/DESCRIPTION’ ... OK
* preparing ‘SUITOR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* 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
* building ‘SUITOR_0.99.1.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('SUITOR')
===============================
This is BiocCheckGitClone version 1.31.36. 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 ‘/Users/pkgbuild/packagebuilder/workers/jobs/2515/SUITOR_20220309132327/SUITOR.Rcheck’
* using R Under development (unstable) (2022-03-02 r81842)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SUITOR/DESCRIPTION’ ... OK
* this is package ‘SUITOR’ version ‘0.99.1’
* 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 ‘SUITOR’ can be installed ... [12s/18s] 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 ... [12s/15s] OK
* checking Rd files ... [1s/1s] 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [26s/34s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
suitor_extract_WH 21.867 0.132 29.087
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [3s/3s]
[3s/4s] 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('SUITOR_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.31.36. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2515/SUITOR_20220309132327/SUITOR_0.99.1.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpCr2Etf/file9d9860703706/lib" 2>/dev/null' had status 1
* 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 3.5.0 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...
* 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...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import stats, utils, graphics in DESCRIPTION as well as
NAMESPACE.
* 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 SUITOR...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
source_extract_WH.R (line 24, column 47)
source_extract_WH.R (line 28, column 47)
source_extract_WH.R (line 52, column 15)
source_extract_WH.R (line 73, column 13)
source_extract_WH.R (line 108, column 22)
source_extract_WH.R (line 112, column 22)
source.R (line 65, column 21)
source.R (line 67, column 24)
source.R (line 71, column 15)
source.R (line 119, column 13)
source.R (line 210, column 15)
source.R (line 232, column 22)
source.R (line 236, column 22)
source.R (line 262, column 13)
source.R (line 324, column 13)
source.R (line 329, column 15)
source.R (line 354, column 11)
source.R (line 432, column 13)
source.R (line 460, column 13)
source.R (line 465, column 13)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/source_extract_WH.R (line 84, column 14)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/source.R (line 74, column 29)
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/source.R (line 19, column 27)
R/source.R (line 20, column 54)
R/source.R (line 22, column 30)
R/source.R (line 23, column 31)
R/source.R (line 24, column 27)
R/source.R (line 25, column 35)
R/source.R (line 56, column 29)
R/source.R (line 57, column 29)
R/source.R (line 58, column 39)
R/source.R (line 59, column 45)
R/source.R (line 60, column 29)
R/source.R (line 61, column 29)
R/source.R (line 62, column 49)
R/source.R (line 68, column 24)
R/source.R (line 74, column 35)
R/source.R (line 91, column 56)
R/source.R (line 113, column 33)
R/source.R (line 129, column 39)
R/source.R (line 146, column 30)
R/source.R (line 157, column 30)
R/source.R (line 214, column 27)
R/source.R (line 414, column 22)
R/source.R (line 419, column 10)
R/source.R (line 423, column 39)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 2 functions > 50 lines.
The longest 5 functions are:
check_op() (R/source.R, line 24): 60 lines
getSummary() (R/source.R, line 260): 60 lines
default.list() (R/source.R, line 343): 49 lines
suitor_seq_C() (R/source.R, line 214): 46 lines
set_op_par() (R/source.R, line 84): 35 lines
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
12% of man pages use one of these cases.
Found in the following files:
suitor.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
suitor.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; 119 lines (10%) are > 80 characters
long.
First 6 lines:
R/source_extract_WH.R:44 clusterExport(cl=clus, c("extractWH_seq_...
R/source_extract_WH.R:112 ret <- foreach(i=1:n, .verbose=FALSE, .in...
R/source.R:20 if (!is.matrix(data) && !is.data.frame(data)) stop("ERR...
R/source.R:58 if (op$min.rank > op$max.rank) stop("ERROR with option ...
R/source.R:74 if (op$min.rank > m) stop(paste("ERROR: option min.rank...
R/source.R:178 tmp <- .C("C_call_nmf", as.numeric(x), as.integer(ia...
* NOTE: Consider multiples of 4 spaces for line indents, 437
lines(38%) are not.
First 6 lines:
R/source_extract_WH.R:3
R/source_extract_WH.R:4 data <- check_data(data)
R/source_extract_WH.R:5 nr <- nrow(data)
R/source_extract_WH.R:6 nc <- ncol(data)
R/source_extract_WH.R:7 if (!is.list(op)) op <- list()
R/source_extract_WH.R:8 op$min.rank <- rank
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: 2
NOTE count: 10
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
BiocCheck FAILED.
merida1 BUILD BIN output
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===============================
R CMD BUILD
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir SUITOR_0.99.1.tar.gz'
>>>>>>>
* installing *source* package ‘SUITOR’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c SUITOR_init.c -o SUITOR_init.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c source.c -o source.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o SUITOR.so SUITOR_init.o source.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/pkgbuild/packagebuilder/workers/jobs/2515/SUITOR_20220309132327/libdir/00LOCK-SUITOR/00new/SUITOR/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SUITOR)
>>>>>>>
>>>>>>> FIXING LINKS FOR libdir/SUITOR/libs/SUITOR.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "libdir/SUITOR/libs/SUITOR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "libdir/SUITOR/libs/SUITOR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "libdir/SUITOR/libs/SUITOR.so"