Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:03:18 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 2220/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ttgsea 1.12.0 (landing page) Dongmin Jung
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | 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: 1.12.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ttgsea.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ttgsea_1.12.0.tar.gz |
StartedAt: 2024-05-31 09:13:47 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 09:16:39 -0400 (Fri, 31 May 2024) |
EllapsedTime: 172.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ttgsea.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ttgsea.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ttgsea_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ttgsea.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘1.12.0’ * 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 fit_model 25.344 3.006 15.704 predict_model 23.799 2.555 13.775 token_vector 9.604 0.400 6.195 text_token 9.507 0.384 6.123 bi_gru 3.453 0.672 6.303 * 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-3.19-bioc/R/bin/R CMD INSTALL ttgsea ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 (2024-04-24) -- "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") 2024-05-31 09:15:41.630089: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 AVX512F AVX512_VNNI FMA To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags. 2024-05-31 09:15:41.850601: I tensorflow/core/util/util.cc:169] 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`. 2024-05-31 09:15:41.894129: E tensorflow/stream_executor/cuda/cuda_blas.cc:2981] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered 2024-05-31 09:15:42.768036: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer.so.7'; dlerror: libnvinfer.so.7: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/biocbuild/bbs-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server 2024-05-31 09:15:42.768153: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer_plugin.so.7'; dlerror: libnvinfer_plugin.so.7: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/biocbuild/bbs-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server 2024-05-31 09:15:42.768174: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly. 2024-05-31 09:15:44.607715: E tensorflow/stream_executor/cuda/cuda_driver.cc:265] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected 2024-05-31 09:15:44.607800: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (nebbiolo1): /proc/driver/nvidia/version does not exist 2024-05-31 09:15:44.608183: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 AVX512F AVX512_VNNI FMA To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags. 1/45 [..............................] - ETA: 2:25 - loss: 1.3692 - pearson_correlation: -0.0698 3/45 [=>............................] - ETA: 1s - loss: 1.5624 - pearson_correlation: 0.0534 5/45 [==>...........................] - ETA: 1s - loss: 1.5480 - pearson_correlation: 0.0927 7/45 [===>..........................] - ETA: 1s - loss: 1.5587 - pearson_correlation: 0.0619 9/45 [=====>........................] - ETA: 1s - loss: 1.5649 - pearson_correlation: 0.0872 11/45 [======>.......................] - ETA: 1s - loss: 1.5646 - pearson_correlation: 0.0924 13/45 [=======>......................] - ETA: 1s - loss: 1.5451 - pearson_correlation: 0.0946 15/45 [=========>....................] - ETA: 1s - loss: 1.5524 - pearson_correlation: 0.0945 17/45 [==========>...................] - ETA: 1s - loss: 1.5602 - pearson_correlation: 0.1102 19/45 [===========>..................] - ETA: 1s - loss: 1.5610 - pearson_correlation: 0.1168 21/45 [=============>................] - ETA: 0s - loss: 1.5441 - pearson_correlation: 0.1250 23/45 [==============>...............] - ETA: 0s - loss: 1.5305 - pearson_correlation: 0.1257 25/45 [===============>..............] - ETA: 0s - loss: 1.5048 - pearson_correlation: 0.1311 27/45 [=================>............] - ETA: 0s - loss: 1.5276 - pearson_correlation: 0.1299 29/45 [==================>...........] - ETA: 0s - loss: 1.5548 - pearson_correlation: 0.1339 31/45 [===================>..........] - ETA: 0s - loss: 1.5576 - pearson_correlation: 0.1422 33/45 [=====================>........] - ETA: 0s - loss: 1.5588 - pearson_correlation: 0.1372 35/45 [======================>.......] - ETA: 0s - loss: 1.5547 - pearson_correlation: 0.1388 37/45 [=======================>......] - ETA: 0s - loss: 1.5498 - pearson_correlation: 0.1469 39/45 [=========================>....] - ETA: 0s - loss: 1.5492 - pearson_correlation: 0.1425 41/45 [==========================>...] - ETA: 0s - loss: 1.5547 - pearson_correlation: 0.1529 43/45 [===========================>..] - ETA: 0s - loss: 1.5510 - pearson_correlation: 0.1479 45/45 [==============================] - ETA: 0s - loss: 1.5528 - pearson_correlation: 0.1538 45/45 [==============================] - 5s 38ms/step - loss: 1.5528 - pearson_correlation: 0.1538 1/4 [======>.......................] - ETA: 1s 4/4 [==============================] - 0s 9ms/step 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 25ms/step 1/32 [..............................] - ETA: 0s 7/32 [=====>........................] - ETA: 0s 13/32 [===========>..................] - ETA: 0s 18/32 [===============>..............] - ETA: 0s 23/32 [====================>.........] - ETA: 0s 29/32 [==========================>...] - ETA: 0s 32/32 [==============================] - 0s 10ms/step 1/32 [..............................] - ETA: 0s 9/32 [=======>......................] - ETA: 0s 16/32 [==============>...............] - ETA: 0s 21/32 [==================>...........] - ETA: 0s 27/32 [========================>.....] - ETA: 0s 32/32 [==============================] - 0s 8ms/step 1/1 [==============================] - ETA: 0s 1/1 [==============================] - 0s 27ms/step 1/32 [..............................] - ETA: 0s 8/32 [======>.......................] - ETA: 0s 16/32 [==============>...............] - ETA: 0s 23/32 [====================>.........] - ETA: 0s 30/32 [===========================>..] - ETA: 0s 32/32 [==============================] - 0s 7ms/step 1/32 [..............................] - ETA: 0s 8/32 [======>.......................] - ETA: 0s 14/32 [============>.................] - ETA: 0s 20/32 [=================>............] - ETA: 0s 26/32 [=======================>......] - ETA: 0s 32/32 [==============================] - ETA: 0s 32/32 [==============================] - 0s 9ms/step 1/32 [..............................] - ETA: 0s 8/32 [======>.......................] - ETA: 0s 14/32 [============>.................] - ETA: 0s 19/32 [================>.............] - ETA: 0s 26/32 [=======================>......] - ETA: 0s 32/32 [==============================] - 0s 8ms/step 1/32 [..............................] - ETA: 0s 8/32 [======>.......................] - ETA: 0s 15/32 [=============>................] - ETA: 0s 21/32 [==================>...........] - ETA: 0s 27/32 [========================>.....] - ETA: 0s 32/32 [==============================] - 0s 9ms/step [ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ] > > proc.time() user system elapsed 28.593 3.755 18.939
ttgsea.Rcheck/ttgsea-Ex.timings
name | user | system | elapsed | |
bi_gru | 3.453 | 0.672 | 6.303 | |
bi_lstm | 0.217 | 0.004 | 0.221 | |
fit_model | 25.344 | 3.006 | 15.704 | |
metric_pearson_correlation | 0.01 | 0.00 | 0.01 | |
plot_model | 0.183 | 0.012 | 0.189 | |
predict_model | 23.799 | 2.555 | 13.775 | |
sampling_generator | 0.000 | 0.000 | 0.001 | |
text_token | 9.507 | 0.384 | 6.123 | |
token_vector | 9.604 | 0.400 | 6.195 | |