Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-26 11:37 -0400 (Wed, 26 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4691 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4405 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4355 |
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 2162/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ttgsea 1.13.0 (landing page) Dongmin Jung
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
To the developers/maintainers of the ttgsea package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ttgsea.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: ttgsea |
Version: 1.13.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ttgsea.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ttgsea_1.13.0.tar.gz |
StartedAt: 2024-06-26 04:34:58 -0400 (Wed, 26 Jun 2024) |
EndedAt: 2024-06-26 04:37:45 -0400 (Wed, 26 Jun 2024) |
EllapsedTime: 166.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ttgsea.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ttgsea.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ttgsea_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ttgsea.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * 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 * checking for file ‘ttgsea/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ttgsea’ version ‘1.13.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘ttgsea’ 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed predict_model 23.030 1.308 13.644 fit_model 22.234 1.214 14.811 token_vector 9.555 0.405 6.179 text_token 9.531 0.322 6.090 bi_gru 3.764 0.918 5.427 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
ttgsea.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ttgsea ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘ttgsea’ ... ** using staged installation ** R ** 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 (ttgsea)
ttgsea.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(ttgsea) Loading required package: keras > > test_check("ttgsea") 2024-06-26 04:36:52.196604: I tensorflow/core/util/port.cc:110] 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`. 2024-06-26 04:36:52.199821: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2024-06-26 04:36:52.254627: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2024-06-26 04:36:52.255149: I tensorflow/core/platform/cpu_feature_guard.cc:182] 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. 2024-06-26 04:36:53.404801: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT 1/45 [..............................] - ETA: 2:30 - loss: 1.8002 - pearson_correlation: -0.2979 4/45 [=>............................] - ETA: 0s - loss: 1.5080 - pearson_correlation: -0.0932 6/45 [===>..........................] - ETA: 0s - loss: 1.5738 - pearson_correlation: -0.0460 9/45 [=====>........................] - ETA: 0s - loss: 1.5971 - pearson_correlation: -0.0174 12/45 [=======>......................] - ETA: 0s - loss: 1.6103 - pearson_correlation: 0.0612 15/45 [=========>....................] - ETA: 0s - loss: 1.5795 - pearson_correlation: 0.0284 16/45 [=========>....................] - ETA: 0s - loss: 1.5912 - pearson_correlation: 0.0406 18/45 [===========>..................] - ETA: 0s - loss: 1.5763 - pearson_correlation: 0.0702 20/45 [============>.................] - ETA: 0s - loss: 1.5528 - pearson_correlation: 0.0898 23/45 [==============>...............] - ETA: 0s - loss: 1.5472 - pearson_correlation: 0.1071 26/45 [================>.............] - ETA: 0s - loss: 1.5459 - pearson_correlation: 0.1193 29/45 [==================>...........] - ETA: 0s - loss: 1.5507 - pearson_correlation: 0.1147 32/45 [====================>.........] - ETA: 0s - loss: 1.5516 - pearson_correlation: 0.1196 35/45 [======================>.......] - ETA: 0s - loss: 1.5490 - pearson_correlation: 0.1139 37/45 [=======================>......] - ETA: 0s - loss: 1.5569 - pearson_correlation: 0.1203 40/45 [=========================>....] - ETA: 0s - loss: 1.5616 - pearson_correlation: 0.1097 42/45 [===========================>..] - ETA: 0s - loss: 1.5604 - pearson_correlation: 0.1121 44/45 [============================>.] - ETA: 0s - loss: 1.5676 - pearson_correlation: 0.1202 45/45 [==============================] - 5s 26ms/step - loss: 1.5676 - pearson_correlation: 0.1176 1/4 [======>.......................] - ETA: 1s 4/4 [==============================] - 0s 5ms/step 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 24ms/step 1/32 [..............................] - ETA: 0s 13/32 [===========>..................] - ETA: 0s 24/32 [=====================>........] - ETA: 0s 32/32 [==============================] - 0s 4ms/step 1/32 [..............................] - ETA: 0s 14/32 [============>.................] - ETA: 0s 25/32 [======================>.......] - ETA: 0s 32/32 [==============================] - 0s 4ms/step 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 22ms/step 1/32 [..............................] - ETA: 0s 14/32 [============>.................] - ETA: 0s 25/32 [======================>.......] - ETA: 0s 32/32 [==============================] - 0s 4ms/step 1/32 [..............................] - ETA: 0s 14/32 [============>.................] - ETA: 0s 24/32 [=====================>........] - ETA: 0s 32/32 [==============================] - ETA: 0s 32/32 [==============================] - 0s 5ms/step 1/32 [..............................] - ETA: 0s 14/32 [============>.................] - ETA: 0s 27/32 [========================>.....] - ETA: 0s 32/32 [==============================] - 0s 4ms/step 1/32 [..............................] - ETA: 0s 14/32 [============>.................] - ETA: 0s 27/32 [========================>.....] - ETA: 0s 32/32 [==============================] - 0s 4ms/step [ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ] > > proc.time() user system elapsed 23.975 1.933 18.082
ttgsea.Rcheck/ttgsea-Ex.timings
name | user | system | elapsed | |
bi_gru | 3.764 | 0.918 | 5.427 | |
bi_lstm | 0.224 | 0.001 | 0.225 | |
fit_model | 22.234 | 1.214 | 14.811 | |
metric_pearson_correlation | 0.01 | 0.00 | 0.01 | |
plot_model | 0.190 | 0.008 | 0.192 | |
predict_model | 23.030 | 1.308 | 13.644 | |
sampling_generator | 0.001 | 0.000 | 0.001 | |
text_token | 9.531 | 0.322 | 6.090 | |
token_vector | 9.555 | 0.405 | 6.179 | |