nebbiolo1 Summary
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| Package: PanViz |
| Version: 0.99.0 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data PanViz |
| BuildTime: 0 minutes 14.49 seconds |
| CheckCommand: BiocCheckGitClone('PanViz') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings PanViz_0.99.0.tar.gz && BiocCheck('PanViz_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 2 minutes 8.31 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 4858.91 KiB |
| BuildID:: PanViz_20220208141719 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: PanViz. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘PanViz/DESCRIPTION’ ... OK
* preparing ‘PanViz’:
* 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
* building ‘PanViz_0.99.0.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('PanViz')
===============================
This is BiocCheckGitClone version 1.31.34. 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:
PanViz.Rproj
.Rhistory
* 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/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2505/PanViz_20220208141719/PanViz.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 ‘PanViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PanViz’ version ‘0.99.0’
* 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 ‘PanViz’ can be installed ... [2s/2s] 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 ... NOTE
Namespaces in Imports field not imported from:
‘devtools’ ‘hash’ ‘stringi’ ‘svMisc’ ‘tibble’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [4s/4s] NOTE
colour_IMON: no visible global function definition for ‘from’
Undefined global functions or variables:
from
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'GWAS_catalog_tsv_to_dataframe.Rd':
\examples lines wider than 100 characters:
path = system.file("extdata", "gwas-association-downloaded_2021-09-13-EFO_1000649.tsv", package="PanViz")
Rd file 'get_grouped_IMON.Rd':
\examples lines wider than 100 characters:
##getting GWAS Catalog association tsv file and cleaning up using GWAS_catalog_tsv_to_dataframe function:
df <- PanViz::GWAS_catalog_tsv_to_dataframe(file = system.file("extdata", "gwas-association-downloaded_2021-09-13-EFO_1000649.tsv", pac ... [TRUNCATED]
G <- PanViz::get_grouped_IMON(dataframe = df, groupby = "studies", ego = 5, save_file = FALSE, colour_groups = FALSE)
G <- PanViz::get_grouped_IMON(dataframe = df, groupby = "studies", ego = 5, save_file = FALSE, colour_groups = TRUE)
These lines will be truncated in the PDF manual.
* 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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [47s/50s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_grouped_IMON 45.732 0.212 48.614
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [48s/55s]
[48s/55s] 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: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2505/PanViz_20220208141719/PanViz.Rcheck/00check.log’
for details.
===============================
BiocCheck('PanViz_0.99.0.tar.gz')
===============================
This is BiocCheck version 1.31.34. 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/2505/PanViz_20220208141719/PanViz_0.99.0.tar.gz" "/tmp/Rtmp7ZQh4g/file3a5d6f4da4fde8/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...
* 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...
* WARNING: Import tibble, devtools, svMisc, stringi, hash in
NAMESPACE as well as DESCRIPTION.
* 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 PanViz...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
R/get_grouped_IMON.R (line 28, column 31)
R/get_IMON.R (line 21, column 31)
R/NCBI_gene_locations.R (line 24, column 25)
R/Reactions_Get_All.R (line 46, column 27)
R/Reactions_Get_All.R (line 52, column 26)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
adjl_to_G_grouped.R (line 122, column 21)
Genes_Get_All.R (line 27, column 44)
get_compound_hashmap.R (line 24, column 47)
NCBI_gene_locations.R (line 14, column 12)
Reactions_Get_All.R (line 26, column 47)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/adjl_to_G_grouped.R (line 19, column 3)
cat() in R/adjl_to_G_grouped.R (line 67, column 3)
cat() in R/adjl_to_G.R (line 14, column 3)
cat() in R/adjl_to_G.R (line 61, column 3)
cat() in R/colour_IMON.R (line 74, column 3)
cat() in R/colour_IMON.R (line 116, column 3)
cat() in R/Genes_Get_All.R (line 12, column 3)
cat() in R/Genes_Get_All.R (line 47, column 3)
cat() in R/Genes_Get_All.R (line 48, column 3)
cat() in R/get_grouped_IMON.R (line 138, column 3)
cat() in R/get_grouped_IMON.R (line 160, column 5)
cat() in R/get_grouped_IMON.R (line 163, column 5)
cat() in R/get_IMON.R (line 87, column 3)
cat() in R/get_IMON.R (line 113, column 5)
cat() in R/get_IMON.R (line 116, column 5)
cat() in R/Get_Kegg_Data.R (line 24, column 3)
cat() in R/NCBI_dbSNP_query.R (line 11, column 3)
cat() in R/NCBI_gene_locations.R (line 10, column 3)
cat() in R/Reactions_Get_All.R (line 10, column 3)
cat() in R/Reactions_Get_All.R (line 54, column 3)
cat() in R/Reactions_Get_All.R (line 55, column 3)
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/adjl_to_G_grouped.R (line 28, column 14)
R/adjl_to_G_grouped.R (line 122, column 19)
R/adjl_to_G.R (line 23, column 14)
R/adjl_to_G.R (line 74, column 53)
R/adjl_to_G.R (line 75, column 54)
R/adjl_to_G.R (line 77, column 54)
R/adjl_to_G.R (line 78, column 55)
R/adjl_to_G.R (line 80, column 65)
R/adjl_to_G.R (line 81, column 66)
R/dbSNP_query_clean_helper.R (line 22, column 10)
R/decompose_IMON.R (line 18, column 5)
R/decompose_IMON.R (line 25, column 9)
R/decompose_IMON.R (line 31, column 5)
R/ego_IMON.R (line 13, column 10)
R/ego_IMON.R (line 32, column 55)
R/ego_IMON.R (line 33, column 54)
R/ego_IMON.R (line 35, column 56)
R/ego_IMON.R (line 36, column 55)
R/ego_IMON.R (line 38, column 67)
R/ego_IMON.R (line 39, column 66)
R/Genes_Get_All.R (line 11, column 8)
R/Genes_Get_All.R (line 21, column 11)
R/get_compound_hashmap.R (line 19, column 11)
R/Reactions_Get_All.R (line 9, column 8)
R/Reactions_Get_All.R (line 20, column 11)
R/retry.R (line 9, column 12)
R/retry.R (line 10, column 10)
R/retry.R (line 12, column 14)
R/retry.R (line 14, column 11)
R/retry.R (line 18, column 11)
R/retry.R (line 24, column 12)
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/get_grouped_IMON.R (line 58, column 13)
R/get_IMON.R (line 49, column 13)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
times)
suppressWarnings() in R/adjl_to_G_grouped.R (line 100, column
10)
suppressWarnings() in R/NCBI_dbSNP_query.R (line 16, column 29)
suppressWarnings() in R/NCBI_dbSNP_query.R (line 25, column 29)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 5 functions > 50 lines.
The longest 5 functions are:
get_grouped_IMON() (R/get_grouped_IMON.R, line 22): 145 lines
colour_IMON() (R/colour_IMON.R, line 13): 124 lines
adjl_to_G_grouped() (R/adjl_to_G_grouped.R, line 17): 108 lines
get_IMON() (R/get_IMON.R, line 19): 101 lines
adjl_to_G() (R/adjl_to_G.R, line 13): 81 lines
* Checking man page documentation...
* WARNING: Add non-empty \value sections to the following man
pages: man/reaction_cleanup.Rd, man/retry.Rd
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples. The following pages do not:
decompose_IMON.Rd, get_IMON.Rd, Get_Kegg_Data.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
33% of man pages use one of these cases.
Found in the following files:
adjl_to_G_grouped.Rd
adjl_to_G.Rd
colour_IMON.Rd
dbSNP_query_check.Rd
decompose_IMON.Rd
ego_IMON.Rd
gene_cleanup.Rd
Genes_Get_All.Rd
get_compound_hashmap.Rd
Get_Kegg_Data.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
adjl_to_G_grouped.Rd
adjl_to_G.Rd
colour_IMON.Rd
dbSNP_query_check.Rd
decompose_IMON.Rd
ego_IMON.Rd
gene_cleanup.Rd
Genes_Get_All.Rd
get_compound_hashmap.Rd
Get_Kegg_Data.Rd
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 364 lines (16%) are > 80 characters
long.
First 6 lines:
R/adjl_to_G_grouped.R:2 #' @description Internal function that construc...
R/adjl_to_G_grouped.R:3 #' @param adjl_G_S - adjacency list containing ...
R/adjl_to_G_grouped.R:4 #' @param unique_group_names - a list of the un...
R/adjl_to_G_grouped.R:5 #' @param unique_group_cols - a list of unique ...
R/adjl_to_G_grouped.R:6 #' @param group_snps - a recursive list contain...
R/adjl_to_G_grouped.R:7 #' @param colour_groups - boolean: whether or n...
* NOTE: Consider multiples of 4 spaces for line indents, 787
lines(35%) are not.
First 6 lines:
R/adjl_to_G_grouped.R:18 ##loading KEGG network data adjacency lists ...
R/adjl_to_G_grouped.R:19 cat("Generating IMON \n")
R/adjl_to_G_grouped.R:20 ##creating IMON network by building up netwo...
R/adjl_to_G_grouped.R:21 ##creating edgelist dataframe for G_S (SNP -...
R/adjl_to_G_grouped.R:22 G_S <- utils::stack(adjl_G_S)
R/adjl_to_G_grouped.R:23 G_S$values <- paste0("hsa: ", G_S$values) #a...
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...
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: 3
WARNING count: 2
NOTE count: 14
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
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| Package: PanViz |
| Version: 0.99.0 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data PanViz |
| BuildTime: 0 minutes 58.35 seconds |
| CheckCommand: BiocCheckGitClone('PanViz') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PanViz_0.99.0.tar.gz && BiocCheck('PanViz_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 13 minutes 46.35 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh PanViz_0.99.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 6.26 seconds |
| PackageFileSize: 4842.57 KiB |
| BuildID:: PanViz_20220208141719 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: PanViz. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 0. |
merida1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘PanViz/DESCRIPTION’ ... OK
* preparing ‘PanViz’:
* 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
* building ‘PanViz_0.99.0.tar.gz’
merida1 CHECK output
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===============================
BiocCheckGitClone('PanViz')
===============================
This is BiocCheckGitClone version 1.31.34. 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:
PanViz.Rproj
.Rhistory
* 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/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2505/PanViz_20220208141719/PanViz.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PanViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PanViz’ version ‘0.99.0’
* 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 ‘PanViz’ can be installed ... [8s/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 ... NOTE
Namespaces in Imports field not imported from:
‘devtools’ ‘hash’ ‘stringi’ ‘svMisc’ ‘tibble’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [13s/23s] NOTE
colour_IMON: no visible global function definition for ‘from’
Undefined global functions or variables:
from
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'GWAS_catalog_tsv_to_dataframe.Rd':
\examples lines wider than 100 characters:
path = system.file("extdata", "gwas-association-downloaded_2021-09-13-EFO_1000649.tsv", package="PanViz")
Rd file 'get_grouped_IMON.Rd':
\examples lines wider than 100 characters:
##getting GWAS Catalog association tsv file and cleaning up using GWAS_catalog_tsv_to_dataframe function:
df <- PanViz::GWAS_catalog_tsv_to_dataframe(file = system.file("extdata", "gwas-association-downloaded_2021-09-13-EFO_1000649.tsv", pac ... [TRUNCATED]
G <- PanViz::get_grouped_IMON(dataframe = df, groupby = "studies", ego = 5, save_file = FALSE, colour_groups = FALSE)
G <- PanViz::get_grouped_IMON(dataframe = df, groupby = "studies", ego = 5, save_file = FALSE, colour_groups = TRUE)
These lines will be truncated in the PDF manual.
* 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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [194s/401s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_grouped_IMON 189.018 1.605 392.844
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [190s/306s]
[191s/307s] 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: 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2505/PanViz_20220208141719/PanViz.Rcheck/00check.log’
for details.
===============================
BiocCheck('PanViz_0.99.0.tar.gz')
===============================
This is BiocCheck version 1.31.34. 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/2505/PanViz_20220208141719/PanViz_0.99.0.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmplCDMCx/file6a616101379e/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...
* 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...
* WARNING: Import tibble, devtools, svMisc, stringi, hash in
NAMESPACE as well as DESCRIPTION.
* 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 PanViz...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
R/get_grouped_IMON.R (line 28, column 31)
R/get_IMON.R (line 21, column 31)
R/NCBI_gene_locations.R (line 24, column 25)
R/Reactions_Get_All.R (line 46, column 27)
R/Reactions_Get_All.R (line 52, column 26)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
adjl_to_G_grouped.R (line 122, column 21)
Genes_Get_All.R (line 27, column 44)
get_compound_hashmap.R (line 24, column 47)
NCBI_gene_locations.R (line 14, column 12)
Reactions_Get_All.R (line 26, column 47)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/adjl_to_G_grouped.R (line 19, column 3)
cat() in R/adjl_to_G_grouped.R (line 67, column 3)
cat() in R/adjl_to_G.R (line 14, column 3)
cat() in R/adjl_to_G.R (line 61, column 3)
cat() in R/colour_IMON.R (line 74, column 3)
cat() in R/colour_IMON.R (line 116, column 3)
cat() in R/Genes_Get_All.R (line 12, column 3)
cat() in R/Genes_Get_All.R (line 47, column 3)
cat() in R/Genes_Get_All.R (line 48, column 3)
cat() in R/get_grouped_IMON.R (line 138, column 3)
cat() in R/get_grouped_IMON.R (line 160, column 5)
cat() in R/get_grouped_IMON.R (line 163, column 5)
cat() in R/get_IMON.R (line 87, column 3)
cat() in R/get_IMON.R (line 113, column 5)
cat() in R/get_IMON.R (line 116, column 5)
cat() in R/Get_Kegg_Data.R (line 24, column 3)
cat() in R/NCBI_dbSNP_query.R (line 11, column 3)
cat() in R/NCBI_gene_locations.R (line 10, column 3)
cat() in R/Reactions_Get_All.R (line 10, column 3)
cat() in R/Reactions_Get_All.R (line 54, column 3)
cat() in R/Reactions_Get_All.R (line 55, column 3)
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/adjl_to_G_grouped.R (line 28, column 14)
R/adjl_to_G_grouped.R (line 122, column 19)
R/adjl_to_G.R (line 23, column 14)
R/adjl_to_G.R (line 74, column 53)
R/adjl_to_G.R (line 75, column 54)
R/adjl_to_G.R (line 77, column 54)
R/adjl_to_G.R (line 78, column 55)
R/adjl_to_G.R (line 80, column 65)
R/adjl_to_G.R (line 81, column 66)
R/dbSNP_query_clean_helper.R (line 22, column 10)
R/decompose_IMON.R (line 18, column 5)
R/decompose_IMON.R (line 25, column 9)
R/decompose_IMON.R (line 31, column 5)
R/ego_IMON.R (line 13, column 10)
R/ego_IMON.R (line 32, column 55)
R/ego_IMON.R (line 33, column 54)
R/ego_IMON.R (line 35, column 56)
R/ego_IMON.R (line 36, column 55)
R/ego_IMON.R (line 38, column 67)
R/ego_IMON.R (line 39, column 66)
R/Genes_Get_All.R (line 11, column 8)
R/Genes_Get_All.R (line 21, column 11)
R/get_compound_hashmap.R (line 19, column 11)
R/Reactions_Get_All.R (line 9, column 8)
R/Reactions_Get_All.R (line 20, column 11)
R/retry.R (line 9, column 12)
R/retry.R (line 10, column 10)
R/retry.R (line 12, column 14)
R/retry.R (line 14, column 11)
R/retry.R (line 18, column 11)
R/retry.R (line 24, column 12)
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/get_grouped_IMON.R (line 58, column 13)
R/get_IMON.R (line 49, column 13)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
times)
suppressWarnings() in R/adjl_to_G_grouped.R (line 100, column
10)
suppressWarnings() in R/NCBI_dbSNP_query.R (line 16, column 29)
suppressWarnings() in R/NCBI_dbSNP_query.R (line 25, column 29)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 5 functions > 50 lines.
The longest 5 functions are:
get_grouped_IMON() (R/get_grouped_IMON.R, line 22): 145 lines
colour_IMON() (R/colour_IMON.R, line 13): 124 lines
adjl_to_G_grouped() (R/adjl_to_G_grouped.R, line 17): 108 lines
get_IMON() (R/get_IMON.R, line 19): 101 lines
adjl_to_G() (R/adjl_to_G.R, line 13): 81 lines
* Checking man page documentation...
* WARNING: Add non-empty \value sections to the following man
pages: man/reaction_cleanup.Rd, man/retry.Rd
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples. The following pages do not:
decompose_IMON.Rd, get_IMON.Rd, Get_Kegg_Data.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
33% of man pages use one of these cases.
Found in the following files:
adjl_to_G_grouped.Rd
adjl_to_G.Rd
colour_IMON.Rd
dbSNP_query_check.Rd
decompose_IMON.Rd
ego_IMON.Rd
gene_cleanup.Rd
Genes_Get_All.Rd
get_compound_hashmap.Rd
Get_Kegg_Data.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
adjl_to_G_grouped.Rd
adjl_to_G.Rd
colour_IMON.Rd
dbSNP_query_check.Rd
decompose_IMON.Rd
ego_IMON.Rd
gene_cleanup.Rd
Genes_Get_All.Rd
get_compound_hashmap.Rd
Get_Kegg_Data.Rd
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 364 lines (16%) are > 80 characters
long.
First 6 lines:
R/adjl_to_G_grouped.R:2 #' @description Internal function that construc...
R/adjl_to_G_grouped.R:3 #' @param adjl_G_S - adjacency list containing ...
R/adjl_to_G_grouped.R:4 #' @param unique_group_names - a list of the un...
R/adjl_to_G_grouped.R:5 #' @param unique_group_cols - a list of unique ...
R/adjl_to_G_grouped.R:6 #' @param group_snps - a recursive list contain...
R/adjl_to_G_grouped.R:7 #' @param colour_groups - boolean: whether or n...
* NOTE: Consider multiples of 4 spaces for line indents, 787
lines(35%) are not.
First 6 lines:
R/adjl_to_G_grouped.R:18 ##loading KEGG network data adjacency lists ...
R/adjl_to_G_grouped.R:19 cat("Generating IMON \n")
R/adjl_to_G_grouped.R:20 ##creating IMON network by building up netwo...
R/adjl_to_G_grouped.R:21 ##creating edgelist dataframe for G_S (SNP -...
R/adjl_to_G_grouped.R:22 G_S <- utils::stack(adjl_G_S)
R/adjl_to_G_grouped.R:23 G_S$values <- paste0("hsa: ", G_S$values) #a...
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...
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: 3
WARNING count: 2
NOTE count: 14
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
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir PanViz_0.99.0.tar.gz'
>>>>>>>
* installing *source* package ‘PanViz’ ...
** 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 (PanViz)