Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:35 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the FEAST package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FEAST.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 626/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FEAST 1.0.0 (landing page) Kenong Su
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: FEAST |
Version: 1.0.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FEAST.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FEAST_1.0.0.tar.gz |
StartedAt: 2021-10-14 19:01:02 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 19:04:43 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 220.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FEAST.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FEAST.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FEAST_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/FEAST.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FEAST/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘FEAST’ version ‘1.0.0’ * 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 ‘FEAST’ 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 * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE FEAST: multiple local function definitions for ‘bp_fun’ with different formal arguments SC3_Clust: no visible global function definition for ‘metadata’ Seurat_Clust: no visible global function definition for ‘CreateSeuratObject’ Seurat_Clust: no visible global function definition for ‘NormalizeData’ Seurat_Clust: no visible global function definition for ‘FindVariableFeatures’ Seurat_Clust: no visible global function definition for ‘ScaleData’ Seurat_Clust: no visible global function definition for ‘RunPCA’ Seurat_Clust: no visible global function definition for ‘VariableFeatures’ Seurat_Clust: no visible global function definition for ‘FindNeighbors’ Seurat_Clust: no visible global function definition for ‘FindClusters’ Seurat_Clust: no visible global function definition for ‘Idents’ Visual_Rslt: no visible global function definition for ‘ggbarplot’ Visual_Rslt: no visible global function definition for ‘theme’ Visual_Rslt: no visible global function definition for ‘element_text’ Visual_Rslt: no visible global function definition for ‘ggline’ Visual_Rslt: no visible global function definition for ‘get_palette’ Visual_Rslt: no visible global function definition for ‘scale_y_continuous’ Visual_Rslt: no visible global function definition for ‘guides’ Visual_Rslt: no visible global function definition for ‘guide_legend’ Visual_Rslt: no visible global function definition for ‘ggarrange’ aricode_NMI : entropy: no visible global function definition for ‘sortPairs’ Undefined global functions or variables: CreateSeuratObject FindClusters FindNeighbors FindVariableFeatures Idents NormalizeData RunPCA ScaleData VariableFeatures element_text get_palette ggarrange ggbarplot ggline guide_legend guides metadata scale_y_continuous sortPairs theme * 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/FEAST.Rcheck/00check.log’ for details.
FEAST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL FEAST ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘FEAST’ ... ** 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 cal_3_metrics.c -o cal_3_metrics.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 FEAST.so cal_3_metrics.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-FEAST/00new/FEAST/libs ** R ** data *** moving datasets to lazyload DB ** 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 (FEAST)
FEAST.Rcheck/FEAST-Ex.timings
name | user | system | elapsed | |
Consensus | 0.942 | 0.032 | 0.975 | |
FEAST | 2.422 | 0.404 | 2.246 | |
FEAST_fast | 1.653 | 0.497 | 1.363 | |
Norm_Y | 0.313 | 0.032 | 0.346 | |
Select_Model_short_SC3 | 0.460 | 0.031 | 0.491 | |
Select_Model_short_TSCAN | 0.472 | 0.026 | 0.511 | |
TSCAN_Clust | 0.001 | 0.002 | 0.003 | |
Visual_Rslt | 1.256 | 0.076 | 1.333 | |
Y | 0.198 | 0.006 | 0.203 | |
align_CellType | 0.002 | 0.000 | 0.001 | |
cal_F2 | 1.376 | 0.665 | 2.043 | |
cal_MSE | 0.895 | 0.011 | 0.908 | |
eval_Cluster | 0.007 | 0.000 | 0.007 | |
process_Y | 0.188 | 0.019 | 0.208 | |
trueclass | 0.002 | 0.002 | 0.004 | |