Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-07 20:25 -0400 (Fri, 07 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" | 4672 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4407 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4434 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4387 |
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 536/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DeProViR 1.1.0 (landing page) Matineh Rahmatbakhsh
| 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 | OK | ERROR | skipped | skipped | |||||||||
To the developers/maintainers of the DeProViR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DeProViR.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: DeProViR |
Version: 1.1.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DeProViR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DeProViR_1.1.0.tar.gz |
StartedAt: 2024-06-05 22:24:24 -0400 (Wed, 05 Jun 2024) |
EndedAt: 2024-06-05 22:34:44 -0400 (Wed, 05 Jun 2024) |
EllapsedTime: 620.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DeProViR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DeProViR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DeProViR_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/DeProViR.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 ‘DeProViR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DeProViR’ 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 for sufficient/correct file permissions ... OK * checking whether package ‘DeProViR’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 encodeHostSeq 69.096 2.434 72.728 predInteractions 58.708 0.566 58.720 encodeViralSeq 56.227 0.851 57.075 gloveImport 55.524 0.788 56.311 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/DeProViR.Rcheck/00check.log’ for details.
DeProViR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL DeProViR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘DeProViR’ ... ** using staged installation ** R ** 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 (DeProViR)
DeProViR.Rcheck/tests/runTests.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. > BiocGenerics:::testPackage('DeProViR') 2024-06-05 22:31:00.365193: 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`. 2024-06-05 22:31:00.369539: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2024-06-05 22:31:00.465428: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2024-06-05 22:31:00.465983: 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. 2024-06-05 22:31:01.573097: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT 2024-06-05 22:31:04.412897: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_2_grad/concat/split_2/split_dim' with dtype int32 [[{{node gradients/split_2_grad/concat/split_2/split_dim}}]] 2024-06-05 22:31:04.414225: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_grad/concat/split/split_dim' with dtype int32 [[{{node gradients/split_grad/concat/split/split_dim}}]] 2024-06-05 22:31:04.415427: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_1_grad/concat/split_1/split_dim' with dtype int32 [[{{node gradients/split_1_grad/concat/split_1/split_dim}}]] 2024-06-05 22:31:04.573271: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/ReverseV2_grad/ReverseV2/ReverseV2/axis' with dtype int32 and shape [1] [[{{node gradients/ReverseV2_grad/ReverseV2/ReverseV2/axis}}]] 2024-06-05 22:31:04.625146: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_2_grad/concat/split_2/split_dim' with dtype int32 [[{{node gradients/split_2_grad/concat/split_2/split_dim}}]] 2024-06-05 22:31:04.626508: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_grad/concat/split/split_dim' with dtype int32 [[{{node gradients/split_grad/concat/split/split_dim}}]] 2024-06-05 22:31:04.627745: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_1_grad/concat/split_1/split_dim' with dtype int32 [[{{node gradients/split_1_grad/concat/split_1/split_dim}}]] 2024-06-05 22:31:04.924850: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_2_grad/concat/split_2/split_dim' with dtype int32 [[{{node gradients/split_2_grad/concat/split_2/split_dim}}]] 2024-06-05 22:31:04.926116: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_grad/concat/split/split_dim' with dtype int32 [[{{node gradients/split_grad/concat/split/split_dim}}]] 2024-06-05 22:31:04.927283: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_1_grad/concat/split_1/split_dim' with dtype int32 [[{{node gradients/split_1_grad/concat/split_1/split_dim}}]] 2024-06-05 22:31:05.084194: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/ReverseV2_grad/ReverseV2/ReverseV2/axis' with dtype int32 and shape [1] [[{{node gradients/ReverseV2_grad/ReverseV2/ReverseV2/axis}}]] 2024-06-05 22:31:05.139521: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_2_grad/concat/split_2/split_dim' with dtype int32 [[{{node gradients/split_2_grad/concat/split_2/split_dim}}]] 2024-06-05 22:31:05.140827: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_grad/concat/split/split_dim' with dtype int32 [[{{node gradients/split_grad/concat/split/split_dim}}]] 2024-06-05 22:31:05.142029: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_1_grad/concat/split_1/split_dim' with dtype int32 [[{{node gradients/split_1_grad/concat/split_1/split_dim}}]] Setting levels: control = 0, case = 1 Setting direction: controls < cases RUNIT TEST PROTOCOL -- Wed Jun 5 22:31:06 2024 *********************************************** Number of test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : DeProViR RUnit Tests - 3 test functions, 0 errors, 0 failures Number of test functions: 3 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 72.955 3.526 76.239
DeProViR.Rcheck/DeProViR-Ex.timings
name | user | system | elapsed | |
encodeHostSeq | 69.096 | 2.434 | 72.728 | |
encodeViralSeq | 56.227 | 0.851 | 57.075 | |
gloveImport | 55.524 | 0.788 | 56.311 | |
loadPreTrainedModel | 1.346 | 0.060 | 1.391 | |
loadTrainingSet | 0.008 | 0.004 | 0.011 | |
performancePlots | 0.732 | 0.024 | 0.756 | |
predInteractions | 58.708 | 0.566 | 58.720 | |