merida1 Summary
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| Package: BiocHail |
| Version: 0.99.15 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data BiocHail |
| BuildTime: 3 minutes 2.15 seconds |
| CheckCommand: |
| CheckTime: |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: -1.00 KiB |
| BuildID:: BiocHail_20230321135853 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: BiocHail. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 1. |
merida1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘BiocHail/DESCRIPTION’ ... OK
* preparing ‘BiocHail’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘gwas_tut.Rmd’ using rmarkdown
2023-03-21 13:59:46.819 WARN NativeCodeLoader:60 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
Initializing Hail with default parameters...
2023-03-21 13:59:48.374 WARN SparkContext:69 - Another SparkContext is being constructed (or threw an exception in its constructor). This may indicate an error, since only one SparkContext should be running in this JVM (see SPARK-2243). The other SparkContext was created at:
org.apache.spark.SparkContext.<init>(SparkContext.scala:85)
is.hail.backend.spark.SparkBackend$.configureAndCreateSparkContext(SparkBackend.scala:148)
is.hail.backend.spark.SparkBackend$.apply(SparkBackend.scala:230)
is.hail.backend.spark.SparkBackend.apply(SparkBackend.scala)
java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
java.base/java.lang.reflect.Method.invoke(Method.java:577)
py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
py4j.Gateway.invoke(Gateway.java:282)
py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
py4j.commands.CallCommand.execute(CallCommand.java:79)
py4j.GatewayConnection.run(GatewayConnection.java:238)
java.base/java.lang.Thread.run(Thread.java:833)
Quitting from lines 57-61 (gwas_tut.Rmd)
Error: processing vignette 'gwas_tut.Rmd' failed with diagnostics:
py4j.protocol.Py4JJavaError: An error occurred while calling z:is.hail.backend.spark.SparkBackend.apply.
<... omitted ...>ke(ReflectionEngine.java:357)
at py4j.Gateway.invoke(Gateway.java:282)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:238)
at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.ExceptionInInitializerError: Exception java.lang.IllegalAccessError: class org.apache.spark.storage.StorageUtils$ (in unnamed module @0x6671dc81) cannot access class sun.nio.ch.DirectBuffer (in module java.base) because module java.base does not export sun.nio.ch to unnamed module @0x6671dc81 [in thread "Thread-3"]
at org.apache.spark.storage.StorageUtils$.<init>(StorageUtils.scala:213)
at org.apache.spark.storage.StorageUtils$.<clinit>(StorageUtils.scala)
... 19 more
See `reticulate::py_last_error()` for details
--- failed re-building ‘gwas_tut.Rmd’
--- re-building ‘large_t2t.Rmd’ using rmarkdown
2023-03-21 13:59:48.495 WARN SparkContext:69 - Another SparkContext is being constructed (or threw an exception in its constructor). This may indicate an error, since only one SparkContext should be running in this JVM (see SPARK-2243). The other SparkContext was created at:
org.apache.spark.SparkContext.<init>(SparkContext.scala:85)
is.hail.backend.spark.SparkBackend$.configureAndCreateSparkContext(SparkBackend.scala:148)
is.hail.backend.spark.SparkBackend$.apply(SparkBackend.scala:230)
is.hail.backend.spark.SparkBackend.apply(SparkBackend.scala)
java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
java.base/java.lang.reflect.Method.invoke(Method.java:577)
py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
py4j.Gateway.invoke(Gateway.java:282)
py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
py4j.commands.CallCommand.execute(CallCommand.java:79)
py4j.GatewayConnection.run(GatewayConnection.java:238)
java.base/java.lang.Thread.run(Thread.java:833)
Initializing Hail with default parameters...
2023-03-21 13:59:48.544 WARN SparkContext:69 - Another SparkContext is being constructed (or threw an exception in its constructor). This may indicate an error, since only one SparkContext should be running in this JVM (see SPARK-2243). The other SparkContext was created at:
org.apache.spark.SparkContext.<init>(SparkContext.scala:85)
is.hail.backend.spark.SparkBackend$.configureAndCreateSparkContext(SparkBackend.scala:148)
is.hail.backend.spark.SparkBackend$.apply(SparkBackend.scala:230)
is.hail.backend.spark.SparkBackend.apply(SparkBackend.scala)
java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
java.base/java.lang.reflect.Method.invoke(Method.java:577)
py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
py4j.Gateway.invoke(Gateway.java:282)
py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
py4j.commands.CallCommand.execute(CallCommand.java:79)
py4j.GatewayConnection.run(GatewayConnection.java:238)
java.base/java.lang.Thread.run(Thread.java:833)
Quitting from lines 65-75 (large_t2t.Rmd)
Error: processing vignette 'large_t2t.Rmd' failed with diagnostics:
py4j.protocol.Py4JJavaError: An error occurred while calling z:is.hail.backend.spark.SparkBackend.apply.
<... omitted ...>ke(ReflectionEngine.java:357)
at py4j.Gateway.invoke(Gateway.java:282)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:238)
at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.ExceptionInInitializerError: Exception java.lang.IllegalAccessError: class org.apache.spark.storage.StorageUtils$ (in unnamed module @0x6671dc81) cannot access class sun.nio.ch.DirectBuffer (in module java.base) because module java.base does not export sun.nio.ch to unnamed module @0x6671dc81 [in thread "Thread-3"]
at org.apache.spark.storage.StorageUtils$.<init>(StorageUtils.scala:213)
at org.apache.spark.storage.StorageUtils$.<clinit>(StorageUtils.scala)
... 19 more
See `reticulate::py_last_error()` for details
--- failed re-building ‘large_t2t.Rmd’
--- re-building ‘ukbb.Rmd’ using rmarkdown
2023-03-21 13:59:48.666 WARN SparkContext:69 - Another SparkContext is being constructed (or threw an exception in its constructor). This may indicate an error, since only one SparkContext should be running in this JVM (see SPARK-2243). The other SparkContext was created at:
org.apache.spark.SparkContext.<init>(SparkContext.scala:85)
is.hail.backend.spark.SparkBackend$.configureAndCreateSparkContext(SparkBackend.scala:148)
is.hail.backend.spark.SparkBackend$.apply(SparkBackend.scala:230)
is.hail.backend.spark.SparkBackend.apply(SparkBackend.scala)
java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
java.base/java.lang.reflect.Method.invoke(Method.java:577)
py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
py4j.Gateway.invoke(Gateway.java:282)
py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
py4j.commands.CallCommand.execute(CallCommand.java:79)
py4j.GatewayConnection.run(GatewayConnection.java:238)
java.base/java.lang.Thread.run(Thread.java:833)
Initializing Hail with default parameters...
2023-03-21 14:02:18.767 WARN SparkContext:69 - Another SparkContext is being constructed (or threw an exception in its constructor). This may indicate an error, since only one SparkContext should be running in this JVM (see SPARK-2243). The other SparkContext was created at:
org.apache.spark.SparkContext.<init>(SparkContext.scala:85)
is.hail.backend.spark.SparkBackend$.configureAndCreateSparkContext(SparkBackend.scala:148)
is.hail.backend.spark.SparkBackend$.apply(SparkBackend.scala:230)
is.hail.backend.spark.SparkBackend.apply(SparkBackend.scala)
java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
java.base/java.lang.reflect.Method.invoke(Method.java:577)
py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
py4j.Gateway.invoke(Gateway.java:282)
py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
py4j.commands.CallCommand.execute(CallCommand.java:79)
py4j.GatewayConnection.run(GatewayConnection.java:238)
java.base/java.lang.Thread.run(Thread.java:833)
Quitting from lines 38-42 (ukbb.Rmd)
Error: processing vignette 'ukbb.Rmd' failed with diagnostics:
py4j.protocol.Py4JJavaError: An error occurred while calling z:is.hail.backend.spark.SparkBackend.apply.
<... omitted ...>ke(ReflectionEngine.java:357)
at py4j.Gateway.invoke(Gateway.java:282)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:238)
at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.ExceptionInInitializerError: Exception java.lang.IllegalAccessError: class org.apache.spark.storage.StorageUtils$ (in unnamed module @0x6671dc81) cannot access class sun.nio.ch.DirectBuffer (in module java.base) because module java.base does not export sun.nio.ch to unnamed module @0x6671dc81 [in thread "Thread-3"]
at org.apache.spark.storage.StorageUtils$.<init>(StorageUtils.scala:213)
at org.apache.spark.storage.StorageUtils$.<clinit>(StorageUtils.scala)
... 19 more
See `reticulate::py_last_error()` for details
--- failed re-building ‘ukbb.Rmd’
SUMMARY: processing the following files failed:
‘gwas_tut.Rmd’ ‘large_t2t.Rmd’ ‘ukbb.Rmd’
Error: Vignette re-building failed.
Execution halted
merida1 CHECK output
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merida1 BUILD BIN output
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nebbiolo1 Summary
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| Package: BiocHail |
| Version: 0.99.15 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BiocHail |
| BuildTime: 2 minutes 44.64 seconds |
| CheckCommand: BiocCheckGitClone('BiocHail') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2947/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2947/BiocHail_20230321135853/BiocHail.install-out.txt BiocHail_0.99.15.tar.gz && BiocCheck('BiocHail_0.99.15.tar.gz', `new-package`=TRUE) |
| CheckTime: 2 minutes 31.78 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 1737.31 KiB |
| BuildID:: BiocHail_20230321135853 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: BiocHail. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘BiocHail/DESCRIPTION’ ... OK
* preparing ‘BiocHail’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘BiocHail_0.99.15.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('BiocHail')
===============================
─ BiocCheckVersion: 1.35.13
─ BiocVersion: 3.17
─ Package: BiocHail
─ PackageVersion: 0.99.15
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2947/BiocHail_20230321135853/BiocHail
─ 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 ‘/home/pkgbuild/packagebuilder/workers/jobs/2947/BiocHail_20230321135853/BiocHail.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocHail/DESCRIPTION’ ... OK
* this is package ‘BiocHail’ version ‘0.99.15’
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BiocHail’ can be installed ... OK
* checking installed package size ... OK
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [7s/7s] OK
* 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 ... NOTE
S3 methods shown with full name in documentation object 'as.data.frame.default':
‘as.data.frame.default’
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [88s/85s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_ukbb_sumstat_10kloci_mt 35.197 10.452 46.448
as.data.frame.hail.table.Table 10.408 23.877 17.195
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.R’ [40s/14s]
[40s/14s] 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 ... [3s/3s] OK
* DONE
Status: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2947/BiocHail_20230321135853/BiocHail.Rcheck/00check.log’
for details.
===============================
BiocCheck('BiocHail_0.99.15.tar.gz')
===============================
─ BiocCheckVersion: 1.35.13
─ BiocVersion: 3.17
─ Package: BiocHail
─ PackageVersion: 0.99.15
─ sourceDir: /tmp/RtmpNVfEBi/filecad6f3020931e/BiocHail
─ installDir: /tmp/RtmpNVfEBi/filecad6f2ebd7c32
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2947/BiocHail_20230321135853/BiocHail.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...
* NOTE: Update R version dependency from 4.2 to 4.3.0.
* 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...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* NOTE: The Description field in the DESCRIPTION is made up by less
than 3 sentences. Please consider expanding this field, and
structure it as a full paragraph
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of BiocHail...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* WARNING: Non-empty \value sections found in man pages.
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 7% of man pages use at least one of these tags.
* NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* 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; 124 lines (6%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 204 lines
(10%) 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 ──
1 ERRORS | 1 WARNINGS | 11 NOTES
See the BiocHail.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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