############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenProSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GenProSeq_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GenProSeq.Rcheck’ * using R Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 LTS * using session charset: UTF-8 * checking for file ‘GenProSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GenProSeq’ version ‘1.3.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions 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 ‘GenProSeq’ 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 R 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 ... NOTE fit_VAE: no visible binding for global variable ‘z_mean’ fit_VAE: no visible binding for global variable ‘z_log_stddev’ fit_VAE : vae_loss: no visible binding for global variable ‘z_log_stddev’ fit_VAE : vae_loss: no visible binding for global variable ‘z_mean’ layer_embedding_token_position : : no visible global function definition for ‘super’ layer_embedding_token_position : : no visible binding for global variable ‘self’ layer_transformer_encoder : : no visible global function definition for ‘super’ layer_transformer_encoder : : no visible binding for global variable ‘self’ Undefined global functions or variables: self super z_log_stddev z_mean * 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 VAE 43.670 3.466 36.547 ART 40.002 2.031 39.500 GAN 15.905 1.056 14.044 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘GenProSeq.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘GenProSeq.Rmd’ using rmarkdown 2023-04-12 06:32:41.482192: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server 2023-04-12 06:32:41.482238: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. 2023-04-12 06:32:45.588320: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set 2023-04-12 06:32:45.589504: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1 2023-04-12 06:32:45.650773: E tensorflow/stream_executor/cuda/cuda_driver.cc:328] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected 2023-04-12 06:32:45.650814: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (nebbiolo2): /proc/driver/nvidia/version does not exist 2023-04-12 06:32:45.651224: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 AVX512F FMA To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags. 2023-04-12 06:32:45.654028: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set 2023-04-12 06:32:45.889030: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:116] None of the MLIR optimization passes are enabled (registered 2) 2023-04-12 06:32:45.890102: I tensorflow/core/platform/profile_utils/cpu_utils.cc:112] CPU Frequency: 2200000000 Hz 1/5 [=====>........................] - ETA: 4s 2/5 [===========>..................] - ETA: 0s 3/5 [=================>............] - ETA: 0s 4/5 [=======================>......] - ETA: 0s 5/5 [==============================] - 2s 178ms/step 1/5 [=====>........................] - ETA: 1s 2/5 [===========>..................] - ETA: 0s 3/5 [=================>............] - ETA: 0s 4/5 [=======================>......] - ETA: 0s 5/5 [==============================] - 1s 111ms/step 1/5 [=====>........................] - ETA: 0s 2/5 [===========>..................] - ETA: 0s 3/5 [=================>............] - ETA: 0s 4/5 [=======================>......] - ETA: 0s 5/5 [==============================] - 1s 106ms/step 1/5 [=====>........................] - ETA: 0s 2/5 [===========>..................] - ETA: 0s 3/5 [=================>............] - ETA: 0s 4/5 [=======================>......] - ETA: 0s 5/5 [==============================] - 1s 101ms/step 1/5 [=====>........................] - ETA: 0s 2/5 [===========>..................] - 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ETA: 0s 4/5 [=======================>......] - ETA: 0s 5/5 [==============================] - 1s 111ms/step 1/5 [=====>........................] - ETA: 0s 2/5 [===========>..................] - ETA: 0s 3/5 [=================>............] - ETA: 0s 4/5 [=======================>......] - ETA: 0s 5/5 [==============================] - 1s 114ms/step 1/5 [=====>........................] - ETA: 0s 2/5 [===========>..................] - ETA: 0s 3/5 [=================>............] - ETA: 0s 4/5 [=======================>......] - ETA: 0s 5/5 [==============================] - 0s 94ms/step 1/5 [=====>........................] - ETA: 0s 2/5 [===========>..................] - ETA: 0s 3/5 [=================>............] - ETA: 0s 4/5 [=======================>......] - ETA: 0s 5/5 [==============================] - 0s 101ms/step 1/5 [=====>........................] - ETA: 0s 2/5 [===========>..................] - ETA: 0s 3/5 [=================>............] - ETA: 0s 4/5 [=======================>......] - ETA: 0s 5/5 [==============================] - 1s 198ms/step 1/5 [=====>........................] - ETA: 0s 2/5 [===========>..................] - ETA: 0s 3/5 [=================>............] - ETA: 0s 4/5 [=======================>......] - ETA: 0s 5/5 [==============================] - 1s 104ms/step 1/5 [=====>........................] - ETA: 0s 2/5 [===========>..................] - ETA: 0s 3/5 [=================>............] - ETA: 0s 4/5 [=======================>......] - ETA: 0s 5/5 [==============================] - 1s 99ms/step 1/5 [=====>........................] - ETA: 0s 2/5 [===========>..................] - ETA: 0s 3/5 [=================>............] - ETA: 0s 4/5 [=======================>......] - ETA: 0s 5/5 [==============================] - 1s 116ms/step 1/5 [=====>........................] - ETA: 0s 2/5 [===========>..................] - ETA: 0s 3/5 [=================>............] - ETA: 0s 4/5 [=======================>......] - ETA: 0s 5/5 [==============================] - 1s 183ms/step 1/5 [=====>........................] - ETA: 0s 2/5 [===========>..................] - ETA: 0s 3/5 [=================>............] - ETA: 0s 4/5 [=======================>......] - ETA: 0s 5/5 [==============================] - 1s 101ms/step 1/5 [=====>........................] - ETA: 0s 2/5 [===========>..................] - ETA: 0s 3/5 [=================>............] - ETA: 0s 4/5 [=======================>......] - ETA: 0s 5/5 [==============================] - 0s 94ms/step 1/5 [=====>........................] - ETA: 0s 2/5 [===========>..................] - ETA: 0s 3/5 [=================>............] - ETA: 0s 4/5 [=======================>......] - ETA: 0s 5/5 [==============================] - 0s 86ms/step Quitting from lines 102-107 (GenProSeq.Rmd) Error: processing vignette 'GenProSeq.Rmd' failed with diagnostics: there is no package called 'ggseqlogo' --- failed re-building ‘GenProSeq.Rmd’ SUMMARY: processing the following file failed: ‘GenProSeq.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/GenProSeq.Rcheck/00check.log’ for details.