Simone Pallotta
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/RGMQL |
| git_branch: RELEASE_3_18 |
| git_last_commit: 5419d1f |
| git_last_commit_date: 2024-03-16 11:16:27 -0400 (Sat, 16 Mar 2024) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:37:12 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 1732/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RGMQL 1.22.1 (landing page) Simone Pallotta
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | ... NOT SUPPORTED ... | ||||||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the RGMQL package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RGMQL.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: RGMQL |
| Version: 1.22.1 |
| Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RGMQL.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings RGMQL_1.22.1.tar.gz |
| StartedAt: 2024-04-16 04:20:19 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 04:25:50 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 331.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: RGMQL.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RGMQL.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings RGMQL_1.22.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/RGMQL.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RGMQL/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RGMQL' version '1.22.1'
* 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 ... 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 ... WARNING
Found the following file with a non-portable file name:
Example of workflows
These are not fully portable file names.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'RGMQL' can be installed ... OK
* checking installed package size ... NOTE
installed size is 90.0Mb
sub-directories of 1Mb or more:
example 89.3Mb
* 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 startup messages can be suppressed ... 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 ... ERROR
Running examples in 'RGMQL-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: take
> ### Title: Method take
> ### Aliases: take take,GMQLDataset-method take-method
>
> ### ** Examples
>
> ## This statement initializes and runs the GMQL server for local execution
> ## and creation of results on disk. Then, with system.file() it defines
> ## the path to the folder "DATASET" in the subdirectory "example"
> ## of the package "RGMQL" and opens such folder as a GMQL dataset
> ## named "rd" using CustomParser
>
> init_gmql()
24/04/16 04:25:25 INFO SparkContext: Running Spark version 2.2.0
24/04/16 04:25:25 INFO SparkContext: Submitted application: GMQL-R
24/04/16 04:25:25 INFO SecurityManager: Changing view acls to: biocbuild
24/04/16 04:25:25 INFO SecurityManager: Changing modify acls to: biocbuild
24/04/16 04:25:25 INFO SecurityManager: Changing view acls groups to:
24/04/16 04:25:25 INFO SecurityManager: Changing modify acls groups to:
24/04/16 04:25:25 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(biocbuild); groups with view permissions: Set(); users with modify permissions: Set(biocbuild); groups with modify permissions: Set()
24/04/16 04:25:26 INFO Utils: Successfully started service 'sparkDriver' on port 58158.
24/04/16 04:25:26 INFO SparkEnv: Registering MapOutputTracker
24/04/16 04:25:26 INFO SparkEnv: Registering BlockManagerMaster
24/04/16 04:25:26 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
24/04/16 04:25:26 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
24/04/16 04:25:26 INFO DiskBlockManager: Created local directory at F:\biocbuild\bbs-3.18-bioc\tmp\blockmgr-a1ddd7e9-fd83-47c3-8db1-8dbf866608cf
24/04/16 04:25:26 INFO MemoryStore: MemoryStore started with capacity 127.2 MB
24/04/16 04:25:26 INFO SparkEnv: Registering OutputCommitCoordinator
24/04/16 04:25:26 INFO Utils: Successfully started service 'SparkUI' on port 4040.
24/04/16 04:25:26 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://10.0.0.5:4040
24/04/16 04:25:26 INFO Executor: Starting executor ID driver on host localhost
24/04/16 04:25:26 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 58159.
24/04/16 04:25:26 INFO NettyBlockTransferService: Server created on 10.0.0.5:58159
24/04/16 04:25:26 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
24/04/16 04:25:26 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 10.0.0.5, 58159, None)
24/04/16 04:25:26 INFO BlockManagerMasterEndpoint: Registering block manager 10.0.0.5:58159 with 127.2 MB RAM, BlockManagerId(driver, 10.0.0.5, 58159, None)
24/04/16 04:25:26 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 10.0.0.5, 58159, None)
24/04/16 04:25:26 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 10.0.0.5, 58159, None)
GMQL Server is up
> test_path <- system.file("example", "DATASET", package = "RGMQL")
> rd = read_gmql(test_path)
>
> ## This statement creates a dataset called 'aggr' which contains one
> ## sample for each antibody_target and cell value found within the metadata
> ## of the 'rd' dataset sample; each created sample contains all regions
> ## from all 'rd' samples with a specific value for their
> ## antibody_target and cell metadata attributes.
>
> aggr = aggregate(rd, conds(c("antibody_target", "cell")))
>
> ## This statement performs the query and returns the resulted dataset as
> ## GRangesList named 'taken'. It returns only the first 45 regions of
> ## each sample present into GRangesList and all the medatata associated
> ## with each sample
>
> taken <- take(aggr, rows = 45)
[OPTIM] variabili da materializzare: 0
24/04/16 04:25:26 INFO MergeMD$: ----------------MergeMD executing..
24/04/16 04:25:26 INFO ReadMD$: ----------------ReadMD executing..
24/04/16 04:25:26 INFO deprecation: mapred.input.dir is deprecated. Instead, use mapreduce.input.fileinputformat.inputdir
24/04/16 04:25:26 INFO deprecation: mapred.max.split.size is deprecated. Instead, use mapreduce.input.fileinputformat.split.maxsize
24/04/16 04:25:37 WARN BlockManager: Putting block broadcast_0 failed due to an exception
24/04/16 04:25:37 WARN BlockManager: Block broadcast_0 could not be removed as it was not found on disk or in memory
Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, :
java.lang.reflect.InaccessibleObjectException: Unable to make field transient java.lang.Object[] java.util.ArrayList.elementData accessible: module java.base does not "opens java.util" to unnamed module @5939a379
Calls: take ... gmql_take -> <Anonymous> -> .jrcall -> .jcall -> .jcheck
Execution halted
* 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 ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
'F:/biocbuild/bbs-3.18-bioc/meat/RGMQL.Rcheck/00check.log'
for details.
RGMQL.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL RGMQL ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library' * installing *source* package 'RGMQL' ... ** 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 (RGMQL)
RGMQL.Rcheck/RGMQL-Ex.timings
| name | user | system | elapsed | |
| aggr-class | 4.89 | 0.86 | 24.10 | |
| aggregate | 0.05 | 0.01 | 0.03 | |
| arrange | 0.04 | 0.00 | 1.15 | |
| collect | 0.03 | 0.00 | 0.03 | |
| compile_query | 0.07 | 0.05 | 1.78 | |
| cover-param-class | 0.08 | 0.00 | 0.06 | |
| cover | 0.07 | 0.01 | 0.41 | |
| delete_dataset | 0 | 0 | 0 | |
| distal-class | 0.11 | 0.02 | 0.07 | |
| download_dataset | 0 | 0 | 0 | |
| execute | 0.02 | 0.01 | 0.03 | |
| export_gmql | 0.62 | 0.05 | 0.67 | |
| extend | 0.08 | 0.00 | 0.05 | |
| filter | 0.11 | 0.00 | 2.22 | |
| filter_and_extract | 1.69 | 0.04 | 1.73 | |
| group_by | 0.08 | 0.00 | 0.91 | |
| import_gmql | 0.17 | 0.00 | 0.17 | |
| init_gmql | 0.01 | 0.00 | 0.17 | |
| log_job | 0.04 | 0.00 | 0.36 | |
| login_gmql | 0.00 | 0.00 | 0.16 | |
| logout_gmql | 0.03 | 0.00 | 0.41 | |
| map | 0.06 | 0.00 | 0.84 | |
| merge | 0.11 | 0.04 | 0.06 | |
| operator-class | 0.19 | 0.01 | 1.55 | |
| ordering-class | 0.05 | 0.00 | 0.04 | |
| read-function | 0.06 | 0.00 | 1.26 | |
| register_gmql | 0 | 0 | 0 | |
| remote_processing | 0 | 0 | 0 | |
| run_query | 0 | 0 | 0 | |
| sample_metadata | 0.03 | 0.00 | 0.50 | |
| sample_region | 0 | 0 | 0 | |
| save_query | 0.01 | 0.00 | 0.89 | |
| select | 0.07 | 0.00 | 0.14 | |
| semijoin | 0.06 | 0.00 | 0.03 | |
| setdiff | 0.06 | 0.00 | 0.06 | |
| show_all_metadata | 0.05 | 0.01 | 0.41 | |
| show_dataset | 0.03 | 0.00 | 6.31 | |
| show_jobs_list | 0.00 | 0.02 | 0.36 | |
| show_queries_list | 0.03 | 0.00 | 0.36 | |
| show_samples_list | 0.02 | 0.00 | 0.35 | |
| show_schema | 0.00 | 0.00 | 0.34 | |
| stop_gmql | 0.09 | 0.01 | 1.73 | |
| stop_job | 0 | 0 | 0 | |