Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-22 11:36:31 -0400 (Wed, 22 May 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" | 4665 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4400 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4427 |
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 2153/2233 | 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 | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
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: 2024-05-21 03:47:39 -0400 (Tue, 21 May 2024) |
EndedAt: 2024-05-21 03:50:29 -0400 (Tue, 21 May 2024) |
EllapsedTime: 169.5 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 22.869 1.320 13.702 fit_model 22.332 1.047 14.849 token_vector 9.651 0.368 6.231 text_token 9.632 0.364 6.193 bi_gru 3.934 0.829 6.206 * 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") 2024-05-21 03:49:35.232756: 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`. 2024-05-21 03:49:35.235653: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2024-05-21 03:49:35.291141: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2024-05-21 03:49:35.291704: 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. 2024-05-21 03:49:36.348405: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT 1/45 [..............................] - ETA: 2:44 - loss: 1.9195 - pearson_correlation: 0.2264 4/45 [=>............................] - ETA: 0s - loss: 1.6730 - pearson_correlation: 0.1469 5/45 [==>...........................] - ETA: 1s - loss: 1.6500 - pearson_correlation: 0.1513 7/45 [===>..........................] - ETA: 1s - loss: 1.5544 - pearson_correlation: 0.1381 9/45 [=====>........................] - ETA: 1s - loss: 1.6209 - pearson_correlation: 0.1202 11/45 [======>.......................] - ETA: 1s - loss: 1.5891 - pearson_correlation: 0.1300 13/45 [=======>......................] - ETA: 1s - loss: 1.5983 - pearson_correlation: 0.1492 15/45 [=========>....................] - ETA: 1s - loss: 1.6026 - pearson_correlation: 0.1545 17/45 [==========>...................] - ETA: 0s - loss: 1.5867 - pearson_correlation: 0.1765 19/45 [===========>..................] - ETA: 0s - loss: 1.5856 - pearson_correlation: 0.1856 21/45 [=============>................] - ETA: 0s - loss: 1.5847 - pearson_correlation: 0.1843 23/45 [==============>...............] - ETA: 0s - loss: 1.5991 - pearson_correlation: 0.2085 25/45 [===============>..............] - ETA: 0s - loss: 1.6006 - pearson_correlation: 0.2137 28/45 [=================>............] - ETA: 0s - loss: 1.6158 - pearson_correlation: 0.2124 30/45 [===================>..........] - ETA: 0s - loss: 1.6020 - pearson_correlation: 0.2248 32/45 [====================>.........] - ETA: 0s - loss: 1.5779 - pearson_correlation: 0.2247 34/45 [=====================>........] - ETA: 0s - loss: 1.5677 - pearson_correlation: 0.2192 36/45 [=======================>......] - ETA: 0s - loss: 1.5703 - pearson_correlation: 0.2125 38/45 [========================>.....] - ETA: 0s - loss: 1.5848 - pearson_correlation: 0.2123 40/45 [=========================>....] - ETA: 0s - loss: 1.5832 - pearson_correlation: 0.2122 43/45 [===========================>..] - ETA: 0s - loss: 1.5777 - pearson_correlation: 0.2187 45/45 [==============================] - ETA: 0s - loss: 1.5666 - pearson_correlation: 0.2068 45/45 [==============================] - 5s 33ms/step - loss: 1.5666 - pearson_correlation: 0.2068 1/4 [======>.......................] - ETA: 1s 4/4 [==============================] - 0s 5ms/step 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 25ms/step 1/32 [..............................] - ETA: 0s 12/32 [==========>...................] - ETA: 0s 22/32 [===================>..........] - ETA: 0s 31/32 [============================>.] - ETA: 0s 32/32 [==============================] - 0s 5ms/step 1/32 [..............................] - ETA: 0s 11/32 [=========>....................] - ETA: 0s 21/32 [==================>...........] - ETA: 0s 30/32 [===========================>..] - ETA: 0s 32/32 [==============================] - 0s 5ms/step 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 26ms/step 1/32 [..............................] - ETA: 0s 10/32 [========>.....................] - ETA: 0s 20/32 [=================>............] - ETA: 0s 28/32 [=========================>....] - ETA: 0s 32/32 [==============================] - 0s 6ms/step 1/32 [..............................] - ETA: 0s 10/32 [========>.....................] - ETA: 0s 18/32 [===============>..............] - ETA: 0s 26/32 [=======================>......] - ETA: 0s 32/32 [==============================] - 0s 6ms/step 1/32 [..............................] - ETA: 1s 12/32 [==========>...................] - ETA: 0s 19/32 [================>.............] - ETA: 0s 27/32 [========================>.....] - ETA: 0s 32/32 [==============================] - 0s 6ms/step 1/32 [..............................] - ETA: 0s 11/32 [=========>....................] - ETA: 0s 21/32 [==================>...........] - ETA: 0s 32/32 [==============================] - ETA: 0s 32/32 [==============================] - 0s 5ms/step [ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ] > > proc.time() user system elapsed 27.010 2.312 18.899
ttgsea.Rcheck/ttgsea-Ex.timings
name | user | system | elapsed | |
bi_gru | 3.934 | 0.829 | 6.206 | |
bi_lstm | 0.207 | 0.013 | 0.219 | |
fit_model | 22.332 | 1.047 | 14.849 | |
metric_pearson_correlation | 0.011 | 0.000 | 0.010 | |
plot_model | 0.189 | 0.005 | 0.187 | |
predict_model | 22.869 | 1.320 | 13.702 | |
sampling_generator | 0.001 | 0.000 | 0.000 | |
text_token | 9.632 | 0.364 | 6.193 | |
token_vector | 9.651 | 0.368 | 6.231 | |