===============================
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_0.99.16.tar.gz’
===============================
BiocCheckGitClone('scMultiSim')
===============================
─ BiocCheckVersion: 1.39.26
─ BiocVersion: 3.19
─ Package: scMultiSim
─ PackageVersion: 0.99.16
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3068/50ca31d190e6032bd67554468e2c7d87959d6ba2/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: (Optional) CITATION file not found. Only include a CITATION
file if there is a preprint or publication for this Bioconductor
package. Note that Bioconductor packages are not required to have
a CITATION file but it is useful both for users and for tracking
Bioconductor project-wide metrics. When including a CITATION
file, add the publication using the 'doi' argument of
'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/3068/50ca31d190e6032bd67554468e2c7d87959d6ba2/scMultiSim.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 22.04.4 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scMultiSim/DESCRIPTION’ ... OK
* this is package ‘scMultiSim’ version ‘0.99.16’
* 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] 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 ... [27s/27s] 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’
.summarizeExp: no visible global function definition for ‘metadata<-’
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’
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 len
len2nfrag max_layers metadata<- 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", "new")
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 ... [44s/44s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [6s/6s]
[7s/7s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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/3068/50ca31d190e6032bd67554468e2c7d87959d6ba2/scMultiSim.Rcheck/00check.log’
for details.
===============================
BiocCheck('scMultiSim_0.99.16.tar.gz')
===============================
─ BiocCheckVersion: 1.39.26
─ BiocVersion: 3.19
─ Package: scMultiSim
─ PackageVersion: 0.99.16
─ sourceDir: /tmp/RtmpCiOBYP/file1d52d36f58c9d5/scMultiSim
─ installDir: /tmp/RtmpCiOBYP/file1d52d36090ac5d
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3068/50ca31d190e6032bd67554468e2c7d87959d6ba2/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 4.3.0 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...
* 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...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (5%).
* 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 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid '<<-' if possible (found 25 times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 27 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 5% of man pages use at least one of these tags.
* 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; 265 lines (5%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 2289 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 | 0 WARNINGS | 8 NOTES
See the scMultiSim.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.