===============================
R CMD BUILD
===============================
* checking for file ‘scMultiSim/DESCRIPTION’ ... OK
* preparing ‘scMultiSim’:
* 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 ‘scMultiSim_0.99.11.tar.gz’
===============================
BiocCheckGitClone('scMultiSim')
===============================
─ BiocCheckVersion: 1.39.18
─ BiocVersion: 3.19
─ Package: scMultiSim
─ PackageVersion: 0.99.11
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3068/6ec61db49244ddb98b83fd3d03d7852efa24e489/scMultiSim
─ 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...
* NOTE: No CITATION file found. Bioconductor packages are not
required to have a CITATION file but it is useful both for users
and for tracking Bioconductor project-wide metrics. If you later
post a preprint or publish a paper about your Bioconductor
package, please add the details with a 'doi' argument in the
CITATION file's 'bibentry()'.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3068/6ec61db49244ddb98b83fd3d03d7852efa24e489/scMultiSim.Rcheck’
* using R Under development (unstable) (2023-11-11 r85510)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scMultiSim/DESCRIPTION’ ... OK
* this is package ‘scMultiSim’ 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 ‘scMultiSim’ 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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/12s] NOTE
.SpatialGrid: no visible global function definition for ‘new’
.amplifyOneCell: no visible binding for global variable ‘len2nfrag’
.atacSeq: no visible binding for global variable ‘dens_nonzero’
.check_opt: no visible binding for global variable ‘val’
.check_opt: no visible binding for global variable ‘checker’
.check_opt: no visible binding for global variable ‘desc’
.check_opt: no visible binding for global variable ‘check’
.check_opt: no visible binding for global variable ‘err_msg’
.check_opt: no visible global function definition for ‘check’
.continuousCIFParamNormal : <anonymous>: no visible binding for global
variable ‘.’
.continuousCIFParamNormal : <anonymous>: no visible binding for global
variable ‘tips’
.continuousCIFParamNormal : <anonymous>: no visible binding for global
variable ‘internal’
.continuousCIFParamNormal : <anonymous> : <anonymous>: no visible
global function definition for ‘Impulsecifpertip’
.continuousCIFParamNormal : <anonymous> : <anonymous>: no visible
binding for global variable ‘tips’
.continuousCIFParamNormal : <anonymous> : <anonymous>: no visible
binding for global variable ‘internal’
.continuousCIFParamSpatial: no visible binding for global variable
‘max_layers’
.continuousCIFParamSpatial: no visible binding for global variable
‘paths’
.continuousCIFParamSpatial: no visible binding for global variable
‘cell_path’
.continuousCIFParamSpatial: no visible binding for global variable
‘path_len’
.continuousCIFParamSpatial: no visible binding for global variable
‘i_cell’
.continuousCIFParamSpatial : <anonymous>: no visible binding for global
variable ‘.’
.continuousCIFParamSpatial : <anonymous>: no visible binding for global
variable ‘i_cell’
.continuousCIFParamSpatial : <anonymous>: no visible binding for global
variable ‘tips’
.continuousCIFParamSpatial : <anonymous>: no visible binding for global
variable ‘internal’
.continuousCIFParamSpatial : <anonymous> : <anonymous>: no visible
global function definition for ‘Impulsecifpertip’
.continuousCIFParamSpatial : <anonymous> : <anonymous>: no visible
binding for global variable ‘tips’
.continuousCIFParamSpatial : <anonymous> : <anonymous>: no visible
binding for global variable ‘internal’
.continuousCIFParamSpatial : <anonymous>: no visible binding for global
variable ‘max_layers’
.continuousCIFParamSpatial : <anonymous>: no visible binding for global
variable ‘paths’
.continuousCIFParamSpatial: no visible binding for global variable ‘id’
.continuousCIFParamSpatial: no visible binding for global variable
‘from’
.continuousCIFParamSpatial: no visible binding for global variable ‘to’
.continuousCIFParamSpatial: no visible binding for global variable
‘len’
.discreteCIF : <anonymous>: no visible binding for global variable ‘.’
.discreteCIFSpatial : <anonymous>: no visible binding for global
variable ‘.’
.dynGRN: no visible global function definition for ‘new’
.geneEffectsByRegulator: no visible binding for global variable
‘target’
.geneEffectsByRegulator: no visible binding for global variable
‘regulator’
.geneEffectsByRegulator: no visible binding for global variable
‘effect’
.getPaths: no visible binding for global variable ‘tips’
.getPaths: no visible binding for global variable ‘internal’
.identityVectors: no visible binding for global variable ‘.’
.print_opt: no visible binding for global variable ‘val’
.print_opt: no visible binding for global variable ‘checker’
.print_opt: no visible binding for global variable ‘desc’
.processVelocity : get_velo: no visible binding for global variable
‘vx_normalized’
.processVelocity : get_velo: no visible binding for global variable
‘vy_normalized’
.processVelocity : get_velo: no visible binding for global variable
‘vx_knn_normalized’
.processVelocity : get_velo: no visible binding for global variable
‘vy_knn_normalized’
.regionToGeneMatrix: no visible binding for global variable ‘.’
.rnaSeq: no visible binding for global variable ‘tips’
.rnaSeq: no visible binding for global variable ‘internal’
.rnaSeq: no visible binding for global variable ‘.’
.rnaSeq: no visible binding for global variable ‘parent’
.rnaSeq: no visible binding for global variable ‘child’
.rnaSeqSpatial: no visible binding for global variable ‘tips’
.rnaSeqSpatial: no visible binding for global variable ‘internal’
.rnaVelocityCosine: no visible binding for global variable
‘current_counts_s_tsne’
.rnaVelocityCosine: no visible binding for global variable
‘future_counts_s_tsne’
.rnaVelocityCosine: no visible binding for global variable ‘vx_raw’
.rnaVelocityCosine: no visible binding for global variable ‘vy_raw’
.rnaVelocityCosine: no visible binding for global variable
‘vx_normalized’
.rnaVelocityCosine: no visible binding for global variable
‘vy_normalized’
.rnaVelocityCosine: no visible binding for global variable ‘vx_knn’
.rnaVelocityCosine: no visible binding for global variable ‘vy_knn’
.rnaVelocityCosine: no visible binding for global variable
‘vx_knn_normalized’
.rnaVelocityCosine: no visible binding for global variable
‘vy_knn_normalized’
.rnaVelocityCosine: no visible binding for global variable
‘future_counts_s_tsne2’
.rnaVelocityCosine: no visible binding for global variable ‘vx_raw2’
.rnaVelocityCosine: no visible binding for global variable ‘vy_raw2’
.rnaVelocityCosine: no visible binding for global variable
‘vx_normalized2’
.rnaVelocityCosine: no visible binding for global variable
‘vy_normalized2’
.rnaVelocityCosine: no visible binding for global variable ‘vx_knn2’
.rnaVelocityCosine: no visible binding for global variable ‘vy_knn2’
.rnaVelocityCosine: no visible binding for global variable
‘vx_knn_normalized2’
.rnaVelocityCosine: no visible binding for global variable
‘vy_knn_normalized2’
.rnaVelocityCosine : <anonymous>: no visible binding for global
variable ‘vx_knn_normalized’
.rnaVelocityCosine : <anonymous>: no visible binding for global
variable ‘vy_knn_normalized’
.rnaVelocityCosine : <anonymous>: no visible binding for global
variable ‘vx_knn_normalized2’
.rnaVelocityCosine : <anonymous>: no visible binding for global
variable ‘vy_knn_normalized2’
.rnaVelocityCosine: no visible binding for global variable ‘x’
.rnaVelocityCosine: no visible binding for global variable ‘y’
add_expr_noise: no visible binding for global variable ‘gene_len_pool’
cci_cell_type_params: no visible binding for global variable ‘tips’
cci_cell_type_params: no visible binding for global variable ‘internal’
gene_corr_cci: no visible binding for global variable ‘name’
gene_corr_cci: no visible binding for global variable ‘value’
gene_corr_regulator: no visible binding for global variable ‘.’
plot_cell_loc: no visible binding for global variable ‘x’
plot_cell_loc: no visible binding for global variable ‘y’
plot_cell_loc: no visible binding for global variable ‘cell_type’
plot_cell_loc: no visible binding for global variable ‘xend’
plot_cell_loc: no visible binding for global variable ‘yend’
plot_grid: no visible binding for global variable ‘x’
plot_grid: no visible binding for global variable ‘y’
plot_grid: no visible binding for global variable ‘index’
plot_rna_velocity: no visible binding for global variable
‘current_counts_s_tsne’
plot_rna_velocity: no visible binding for global variable
‘future_counts_s_tsne’
plot_rna_velocity: no visible binding for global variable ‘vx_raw’
plot_rna_velocity: no visible binding for global variable ‘vy_raw’
plot_rna_velocity: no visible binding for global variable
‘vx_normalized’
plot_rna_velocity: no visible binding for global variable
‘vy_normalized’
plot_rna_velocity: no visible binding for global variable ‘vx_knn’
plot_rna_velocity: no visible binding for global variable ‘vy_knn’
plot_rna_velocity: no visible binding for global variable
‘vx_knn_normalized’
plot_rna_velocity: no visible binding for global variable
‘vy_knn_normalized’
plot_rna_velocity: no visible binding for global variable ‘index’
plot_tsne: no visible binding for global variable ‘x’
plot_tsne: no visible binding for global variable ‘y’
plot_tsne: no visible binding for global variable ‘index’
rna_velo_knn: no visible global function definition for ‘paired_simil’
rna_velo_knn : <anonymous>: no visible global function definition for
‘distMat.KernelKnn’
sim_example: no visible binding for global variable ‘GRN_params_100’
sim_example_spatial: no visible binding for global variable
‘GRN_params_100’
sim_true_counts: no visible binding for global variable ‘.rn_sp’
sim_true_counts: no visible binding for global variable ‘paths’
sim_true_counts: no visible binding for global variable ‘total_ncell’
write_files: no visible binding for global variable ‘methods’
write_files: no visible global function definition for ‘is’
Undefined global functions or variables:
. .rn_sp GRN_params_100 Impulsecifpertip cell_path cell_type check
checker child current_counts_s_tsne dens_nonzero desc
distMat.KernelKnn effect err_msg from future_counts_s_tsne
future_counts_s_tsne2 gene_len_pool i_cell id index internal is len
len2nfrag max_layers methods name new paired_simil parent path_len
paths regulator target tips to total_ncell val value vx_knn vx_knn2
vx_knn_normalized vx_knn_normalized2 vx_normalized vx_normalized2
vx_raw vx_raw2 vy_knn vy_knn2 vy_knn_normalized vy_knn_normalized2
vy_normalized vy_normalized2 vy_raw vy_raw2 x xend y yend
Consider adding
importFrom("methods", "is", "new")
importFrom("utils", "methods")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following calls to data() loading into the global environment:
File ‘scMultiSim/R/6_technoise.R’:
data(len2nfrag)
See section ‘Good practice’ in ‘?data’.
* 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 ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [37s/37s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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 ... [3s/3s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3068/6ec61db49244ddb98b83fd3d03d7852efa24e489/scMultiSim.Rcheck/00check.log’
for details.
===============================
BiocCheck('scMultiSim_0.99.11.tar.gz')
===============================
─ BiocCheckVersion: 1.39.18
─ BiocVersion: 3.19
─ Package: scMultiSim
─ PackageVersion: 0.99.11
─ sourceDir: /tmp/RtmpEC5P9P/fileed2645e64873f/scMultiSim
─ installDir: /tmp/RtmpEC5P9P/fileed264671a0826
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3068/6ec61db49244ddb98b83fd3d03d7852efa24e489/scMultiSim.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 4.4.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, Sequencing, ExperimentalDesign
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
* WARNING: No Bioconductor dependencies detected. Reach out to the
Bioconductor community or consider a CRAN submission.
* Checking for pinned package versions in DESCRIPTION...
* 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 scMultiSim...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid '<<-' if possible (found 25 times)
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 28 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* 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; 275 lines (5%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 2449 lines
(42%) 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 is in the Support Site Watched Tags.
─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 13 NOTES
See the scMultiSim.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.