Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:42 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 1013/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
immApex 1.1.0 (landing page) Nick Borcherding
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the immApex package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/immApex.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: immApex |
Version: 1.1.0 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:immApex.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings immApex_1.1.0.tar.gz |
StartedAt: 2024-12-23 01:41:49 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 01:48:41 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 412.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: immApex.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:immApex.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings immApex_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/immApex.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'immApex/DESCRIPTION' ... OK * this is package 'immApex' version '1.1.0' * 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 whether package 'immApex' 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 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 ... 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 data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed variationalSequences 16.11 5.11 88.03 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'spelling.R' 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: OK
immApex.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL immApex ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'immApex' ... ** using staged installation ** R ** data ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (immApex)
immApex.Rcheck/tests/spelling.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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. > if(requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.21 0.06 0.31
immApex.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(immApex) > > test_check("immApex") 2024-12-23 01:47:42.518543: I tensorflow/core/util/port.cc:153] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`. 2024-12-23 01:47:56.986044: I tensorflow/core/util/port.cc:153] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`. 2024-12-23 01:48:13.420894: I tensorflow/core/platform/cpu_feature_guard.cc:210] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations. To enable the following instructions: AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags. WARNING:tensorflow:From C:\PYTHON~2\Lib\site-packages\keras\src\backend\tensorflow\core.py:204: The name tf.placeholder is deprecated. Please use tf.compat.v1.placeholder instead. [1m1/4[0m [32m━━━━━[0m[37m━━━━━━━━━━━━━━━[0m [1m0s[0m 78ms/step [1m4/4[0m [32m━━━━━━━━━━━━━━━━━━━━[0m[37m[0m [1m0s[0m 21ms/step [1m4/4[0m [32m━━━━━━━━━━━━━━━━━━━━[0m[37m[0m [1m0s[0m 21ms/step [1m1/1[0m [32m━━━━━━━━━━━━━━━━━━━━[0m[37m[0m [1m0s[0m 47ms/step [1m1/1[0m [32m━━━━━━━━━━━━━━━━━━━━[0m[37m[0m [1m0s[0m 63ms/step [ FAIL 0 | WARN 0 | SKIP 2 | PASS 60 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • empty test (2): 'test-getIR.R:3:1', 'test-variationalSequences.R:3:1' [ FAIL 0 | WARN 0 | SKIP 2 | PASS 60 ] > > proc.time() user system elapsed 61.92 17.53 121.54
immApex.Rcheck/immApex-Ex.timings
name | user | system | elapsed | |
adjacencyMatrix | 0 | 0 | 0 | |
formatGenes | 2.03 | 0.43 | 2.46 | |
generateSequences | 0 | 0 | 0 | |
geometricEncoder | 0.23 | 0.37 | 0.60 | |
getIMGT | 0.10 | 0.02 | 3.30 | |
inferCDR | 0.75 | 0.00 | 3.02 | |
mutateSequences | 0 | 0 | 0 | |
onehotEncoder | 0.23 | 0.14 | 1.28 | |
positionalEncoder | 0.02 | 0.00 | 0.01 | |
probabilityMatrix | 0 | 0 | 0 | |
propertyEncoder | 0.01 | 0.00 | 0.02 | |
sequenceDecoder | 0.03 | 0.00 | 0.03 | |
tokenizeSequences | 0 | 0 | 0 | |
variationalSequences | 16.11 | 5.11 | 88.03 | |