Cole Trapnell
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/monocle |
| git_branch: RELEASE_3_13 |
| git_last_commit: dd8f8f2 |
| git_last_commit_date: 2021-05-19 12:05:11 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:12 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the monocle package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/monocle.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1177/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| monocle 2.20.0 (landing page) Cole Trapnell
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: monocle |
| Version: 2.20.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:monocle.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings monocle_2.20.0.tar.gz |
| StartedAt: 2021-10-15 02:12:36 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 02:15:12 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 156.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: monocle.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:monocle.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings monocle_2.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/monocle.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'monocle/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'monocle' version '2.20.0'
* 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 whether package 'monocle' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... WARNING
Namespaces in Imports field not imported from:
'Rcpp' 'biocViews'
All declared Imports should be used.
Missing or unexported object: 'scater::newSCESet'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
assign_cell_lineage: no visible global function definition for 'nei'
buildBranchCellDataSet: no visible global function definition for 'nei'
clusterCells: no visible global function definition for 'quantile'
count_leaf_descendents: no visible global function definition for 'nei'
cth_classifier_cds: no visible global function definition for 'nei'
cth_classifier_cell: no visible global function definition for 'nei'
diff_test_helper: no visible binding for global variable 'Size_Factor'
exportCDS: no visible binding for global variable 'use_for_ordering'
extract_good_ordering: no visible global function definition for 'nei'
fit_model_helper: no visible binding for global variable 'Size_Factor'
get_next_node_id: no visible binding for '<<-' assignment to
'next_node'
get_next_node_id: no visible binding for global variable 'next_node'
make_canonical: no visible global function definition for 'nei'
measure_diameter_path: no visible global function definition for 'nei'
orderCells: no visible binding for '<<-' assignment to 'next_node'
plot_multiple_branches_pseudotime: no visible binding for global
variable 'pseudocount'
plot_multiple_branches_pseudotime: no visible binding for global
variable 'Branch'
project2MST: no visible global function definition for 'nei'
reverseEmbeddingCDS : <anonymous>: no visible global function
definition for 'quantile'
Undefined global functions or variables:
Branch Size_Factor nei next_node pseudocount quantile
use_for_ordering
Consider adding
importFrom("stats", "quantile")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/monocle/libs/i386/monocle.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/monocle/libs/x64/monocle.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following directory looks like a leftover from 'knitr':
'figure'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
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: 1 WARNING, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/monocle.Rcheck/00check.log'
for details.
monocle.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/monocle_2.20.0.tar.gz && rm -rf monocle.buildbin-libdir && mkdir monocle.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=monocle.buildbin-libdir monocle_2.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL monocle_2.20.0.zip && rm monocle_2.20.0.tar.gz monocle_2.20.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 9403k 0 33775 0 0 157k 0 0:00:59 --:--:-- 0:00:59 157k
30 9403k 30 2907k 0 0 2464k 0 0:00:03 0:00:01 0:00:02 2463k
68 9403k 68 6415k 0 0 2939k 0 0:00:03 0:00:02 0:00:01 2938k
100 9403k 100 9403k 0 0 3357k 0 0:00:02 0:00:02 --:--:-- 3357k
install for i386
* installing *source* package 'monocle' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c clustering.cpp -o clustering.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o monocle.dll tmp.def RcppExports.o clustering.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/monocle.buildbin-libdir/00LOCK-monocle/00new/monocle/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'monocle'
finding HTML links ... done
BEAM html
CellDataSet-methods html
CellDataSet html
CellType html
CellTypeHierarchy html
addCellType html
branchTest html
buildBranchCellDataSet html
calABCs html
calILRs html
calibrate_per_cell_total_proposal html
cellPairwiseDistances-set html
cellPairwiseDistances html
clusterCells html
finding level-2 HTML links ... done
clusterGenes html
compareModels html
detectBifurcationPoint html
detectGenes html
diff_test_helper html
differentialGeneTest html
dispersionTable html
estimateDispersionsForCellDataSet html
estimateSizeFactorsForMatrix html
estimate_t html
exportCDS html
extract_good_branched_ordering html
fitModel html
fit_model_helper html
genSmoothCurveResiduals html
genSmoothCurves html
get_classic_muscle_markers html
importCDS html
load_HSMM html
load_HSMM_markers html
load_lung html
markerDiffTable html
mcesApply html
minSpanningTree-set html
minSpanningTree html
newCellDataSet html
newCellTypeHierarchy html
orderCells html
order_p_node html
package-deprecated html
plot_cell_clusters html
plot_cell_trajectory html
plot_clusters html
plot_coexpression_matrix html
plot_complex_cell_trajectory html
plot_genes_branched_heatmap html
plot_genes_branched_pseudotime html
plot_genes_in_pseudotime html
plot_genes_jitter html
plot_genes_positive_cells html
plot_genes_violin html
plot_multiple_branches_heatmap html
plot_multiple_branches_pseudotime html
plot_ordering_genes html
plot_pc_variance_explained html
plot_pseudotime_heatmap html
plot_rho_delta html
pq_helper html
reduceDimension html
reducedDimA-set html
reducedDimA html
reducedDimK-set html
reducedDimK html
reducedDimS-set html
reducedDimS html
reducedDimW-set html
reducedDimW html
relative2abs html
residualMatrix html
responseMatrix html
selectTopMarkers html
setOrderingFilter html
spike_df html
vstExprs html
** 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
install for x64
* installing *source* package 'monocle' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c clustering.cpp -o clustering.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o monocle.dll tmp.def RcppExports.o clustering.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/monocle.buildbin-libdir/monocle/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'monocle' as monocle_2.20.0.zip
* DONE (monocle)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'monocle' successfully unpacked and MD5 sums checked
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monocle.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> #test_check("monocle")
>
> proc.time()
user system elapsed
0.32 0.06 0.37
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monocle.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> #test_check("monocle")
>
> proc.time()
user system elapsed
0.28 0.03 0.29
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monocle.Rcheck/examples_i386/monocle-Ex.timings
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monocle.Rcheck/examples_x64/monocle-Ex.timings
|