Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 557/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
destiny 3.20.0 (landing page) Philipp Angerer
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the destiny package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/destiny.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: destiny |
Version: 3.20.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:destiny.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings destiny_3.20.0.tar.gz |
StartedAt: 2024-11-19 21:25:40 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 21:33:06 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 445.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: destiny.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:destiny.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings destiny_3.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/destiny.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘destiny/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘destiny’ version ‘3.20.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .lintr .vscode These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘destiny’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘rgl’ ‘SingleCellExperiment’ A package should be listed in only one of these fields. 'LinkingTo' for ‘grDevices’ is unused as it has no 'include' directory * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 whether startup messages can be suppressed ... 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 ... OK * checking Rd files ... NOTE checkRd: (-1) Gene-Relevance.Rd:94: Escaped LaTeX specials: \_ * 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 ... NOTE S3 methods shown with full name in Rd file 'coercions.Rd': ‘fortify.DiffusionMap’ ‘fortify.DPT’ S3 methods shown with full name in Rd file 'plot.DPT.Rd': ‘plot.DPT’ S3 methods shown with full name in Rd file 'plot.DiffusionMap.Rd': ‘plot.DiffusionMap’ The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Gene-Relevance-plotting 4.651 0.334 5.012 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ 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 ... OK * DONE Status: 6 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/destiny.Rcheck/00check.log’ for details.
destiny.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL destiny ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘destiny’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/grDevices/include' -I/opt/R/x86_64/include -ggdb -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/grDevices/include' -I/opt/R/x86_64/include -ggdb -fPIC -falign-functions=64 -Wall -g -O2 -c censoring.cpp -o censoring.o censoring.cpp:57:14: warning: variable 'm0' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ censoring.cpp:68:19: note: uninitialized use occurs here * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) ) ^~ censoring.cpp:57:10: note: remove the 'if' if its condition is always true } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ censoring.cpp:57:14: warning: variable 'm0' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized] } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~ censoring.cpp:68:19: note: uninitialized use occurs here * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) ) ^~ censoring.cpp:57:14: note: remove the '&&' if its condition is always true } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~~~~ censoring.cpp:52:12: note: initialize the variable 'm0' to silence this warning double m0, m1; ^ = 0.0 censoring.cpp:57:14: warning: variable 'm1' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ censoring.cpp:68:47: note: uninitialized use occurs here * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) ) ^~ censoring.cpp:57:10: note: remove the 'if' if its condition is always true } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ censoring.cpp:57:14: warning: variable 'm1' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized] } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~ censoring.cpp:68:47: note: uninitialized use occurs here * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) ) ^~ censoring.cpp:57:14: note: remove the '&&' if its condition is always true } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~~~~ censoring.cpp:52:16: note: initialize the variable 'm1' to silence this warning double m0, m1; ^ = 0.0 censoring.cpp:57:14: warning: variable 'use_d' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ censoring.cpp:63:20: note: uninitialized use occurs here const double v = use_d ? d : c; ^~~~~ censoring.cpp:57:10: note: remove the 'if' if its condition is always true } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ censoring.cpp:57:14: warning: variable 'use_d' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized] } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~ censoring.cpp:63:20: note: uninitialized use occurs here const double v = use_d ? d : c; ^~~~~ censoring.cpp:57:14: note: remove the '&&' if its condition is always true } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~~~~ censoring.cpp:18:12: note: initialize the variable 'use_d' to silence this warning bool use_d; ^ = false 6 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/grDevices/include' -I/opt/R/x86_64/include -ggdb -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o destiny.so RcppExports.o censoring.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-destiny/00new/destiny/libs ** R ** data ** demo ** 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 (destiny)
destiny.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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) > library(destiny) > > test_check('destiny') [ FAIL 0 | WARN 0 | SKIP 1 | PASS 67 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • Not yet stable (1): 'test_gr.r:23:2' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 67 ] > > proc.time() user system elapsed 12.669 1.442 14.214
destiny.Rcheck/destiny-Ex.timings
name | user | system | elapsed | |
DPT-matrix-methods | 1.178 | 0.071 | 1.252 | |
DPT-methods | 0.949 | 0.082 | 1.054 | |
DPT | 1.148 | 0.063 | 1.214 | |
DiffusionMap-accessors | 0.261 | 0.056 | 0.318 | |
DiffusionMap-class | 2.416 | 0.078 | 2.506 | |
DiffusionMap-methods | 0.229 | 0.023 | 0.256 | |
ExpressionSet-helpers | 0.088 | 0.003 | 0.091 | |
Gene-Relevance-methods | 1.018 | 0.149 | 1.179 | |
Gene-Relevance-plotting | 4.651 | 0.334 | 5.012 | |
Gene-Relevance | 1.747 | 0.156 | 1.920 | |
Sigmas-class | 0.101 | 0.012 | 0.118 | |
coercions | 0.264 | 0.049 | 0.315 | |
colorlegend | 0.011 | 0.001 | 0.012 | |
cube_helix | 0.005 | 0.001 | 0.007 | |
destiny-generics | 0.276 | 0.077 | 0.358 | |
destiny | 4.797 | 0.080 | 4.900 | |
dm_predict | 0.292 | 0.028 | 0.322 | |
eig_decomp | 0.001 | 0.000 | 0.001 | |
extractions | 0.484 | 0.054 | 0.542 | |
find_dm_k | 0.011 | 0.001 | 0.014 | |
find_sigmas | 0.294 | 0.019 | 0.315 | |
find_tips | 0.250 | 0.041 | 0.293 | |
l_which | 0 | 0 | 0 | |
plot.DPT | 1.267 | 0.060 | 1.332 | |
plot.DiffusionMap | 0.346 | 0.030 | 0.380 | |
plot.Sigmas | 0.139 | 0.046 | 0.186 | |
projection_dist | 0.131 | 0.007 | 0.137 | |
random_root | 0.227 | 0.029 | 0.256 | |