===============================
R CMD BUILD
===============================
* checking for file ‘DeProViR/DESCRIPTION’ ... OK
* preparing ‘DeProViR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘DeProViR_tutorial.Rmd’ using rmarkdown
2023-09-18 17:06:53.884088: 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`.
2023-09-18 17:06:53.886871: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2023-09-18 17:06:53.938434: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2023-09-18 17:06:53.938963: 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.
2023-09-18 17:06:55.021740: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2023-09-18 17:06:59.022222: 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}}]]
2023-09-18 17:06:59.023900: 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}}]]
2023-09-18 17:06:59.025094: 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}}]]
2023-09-18 17:06:59.178547: 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}}]]
2023-09-18 17:06:59.228288: 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}}]]
2023-09-18 17:06:59.229529: 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}}]]
2023-09-18 17:06:59.230672: 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}}]]
2023-09-18 17:06:59.505757: 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}}]]
2023-09-18 17:06:59.507003: 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}}]]
2023-09-18 17:06:59.508150: 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}}]]
2023-09-18 17:06:59.656432: 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}}]]
2023-09-18 17:06:59.705935: 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}}]]
2023-09-18 17:06:59.707181: 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}}]]
2023-09-18 17:06:59.708337: 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}}]]
Quitting from lines 281-292 [unnamed-chunk-4] (DeProViR_tutorial.Rmd)
Error: processing vignette 'DeProViR_tutorial.Rmd' failed with diagnostics:
Input is empty or only contains BOM or terminal control characters
--- failed re-building ‘DeProViR_tutorial.Rmd’
SUMMARY: processing the following file failed:
‘DeProViR_tutorial.Rmd’
Error: Vignette re-building failed.
Execution halted
===============================
R CMD BUILD
===============================
* checking for file ‘DeProViR/DESCRIPTION’ ... OK
* preparing ‘DeProViR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘DeProViR_0.99.10.tar.gz’
===============================
BiocCheckGitClone('DeProViR')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: DeProViR
─ PackageVersion: 0.99.10
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3148/ad9575275801ce91e13db193ee39ac362df29a45/DeProViR
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3148/ad9575275801ce91e13db193ee39ac362df29a45/DeProViR.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DeProViR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeProViR’ version ‘0.99.10’
* 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 serialization versions ... OK
* checking whether package ‘DeProViR’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.0Mb
sub-directories of 1Mb or more:
extdata 5.8Mb
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/4s] OK
* checking use of S3 registration ... 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 ... [12s/13s] NOTE
gloveEmb_import: no visible global function definition for ‘unzip’
Undefined global functions or variables:
unzip
Consider adding
importFrom("utils", "unzip")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... [20s/75s] ERROR
Running examples in ‘DeProViR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: encode_HostSeq
> ### Title: Host Protein Sequence Encoding with GloVe Embedding Vectors
> ### Aliases: encode_HostSeq
>
> ### ** Examples
>
> #download glove index
> zip_url <- "https://nlp.stanford.edu/data/glove.6B.zip"
> #Destination folder to save the downloaded file
> dest_folder = tempdir()
> #Download the zip file
> download.file(zip_url,
+ destfile = file.path(dest_folder, "glove.6B.zip"), mode = "wb")
trying URL 'https://nlp.stanford.edu/data/glove.6B.zip'
Content type 'application/zip' length 862182613 bytes (822.2 MB)
=====
downloaded 98.2 MB
Warning in download.file(zip_url, destfile = file.path(dest_folder, "glove.6B.zip"), :
downloaded length 0 != reported length 0
Warning in download.file(zip_url, destfile = file.path(dest_folder, "glove.6B.zip"), :
URL 'https://downloads.cs.stanford.edu/nlp/data/glove.6B.zip': Timeout of 60 seconds was reached
Error in download.file(zip_url, destfile = file.path(dest_folder, "glove.6B.zip"), :
download from 'https://nlp.stanford.edu/data/glove.6B.zip' failed
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [4s/4s]
[4s/5s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [6s/6s] OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3148/ad9575275801ce91e13db193ee39ac362df29a45/DeProViR.Rcheck/00check.log’
for details.
===============================
BiocCheck('DeProViR_0.99.10.tar.gz')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: DeProViR
─ PackageVersion: 0.99.10
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp3GvTFp/file892476ae1a95/DeProViR
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp3GvTFp/file892444172d52
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3148/ad9575275801ce91e13db193ee39ac362df29a45/DeProViR.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
DataImport
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of DeProViR...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 3 functions greater than 50 lines.
* Checking man page documentation...
Registered S3 methods overwritten by 'fmsb':
method from
print.roc pROC
plot.roc pROC
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 2 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 684 lines
(42%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 9 NOTES
See the DeProViR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir DeProViR_0.99.10.tar.gz'
>>>>>>>
* 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)