Package: RGMQL

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RGMQL.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RGMQL_1.2.0.tar.gz

StartedAt: 2019-04-16 02:20:54 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:24:51 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 236.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RGMQL.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RGMQL.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RGMQL_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/RGMQL.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RGMQL/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RGMQL’ version ‘1.2.0’
* 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 ‘RGMQL’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 20.0Mb
  sub-directories of 1Mb or more:
    example  19.4Mb
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
Error: package or namespace load failed for ‘RGMQL’:
 .onLoad failed in loadNamespace() for 'Rsamtools', details:
  call: (function (classes, fdef, mtable) 
  error: unable to find an inherited method for function ‘strand’ for signature ‘"expressionsIndex"’
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domai
Execution halted
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘RGMQL/R/onLoad.R’:
  .onLoad calls:
    packageStartupMessage("Check if GMQL credentials are expired... \n")

See section ‘Good practice’ in '?.onAttach'.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
aggr-class   9.203  0.912   4.204
take         6.796  0.739   2.496
show_dataset 0.062  0.015  11.122
* 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/RGMQL.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RGMQL
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘RGMQL’ ...
** 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
* DONE (RGMQL)

name	user	system	elapsed
aggr-class	9.203	0.912	4.204
aggregate	0.143	0.005	0.039
arrange	0.163	0.005	0.046
collect	0.136	0.006	0.042
compile_query	1.913	0.041	2.156
cover-param-class	0.112	0.016	0.087
cover	0.074	0.010	0.052
delete_dataset	0	0	0
distal-class	0.104	0.010	0.101
download_dataset	0.001	0.001	0.000
execute	0.055	0.006	0.047
export_gmql	1.302	0.039	1.368
extend	0.060	0.004	0.050
filter	0.169	0.012	0.126
filter_and_extract	0.597	0.054	0.690
group_by	0.093	0.014	0.102
import_gmql	0.170	0.028	0.221
init_gmql	0.036	0.005	0.205
log_job	0.027	0.004	0.324
login_gmql	0.014	0.001	0.182
map	0.088	0.011	0.069
merge	0.102	0.012	0.072
operator-class	0.236	0.024	0.173
ordering-class	0.144	0.006	0.059
read-function	0.183	0.013	0.387
register_gmql	0	0	0
remote_processing	0.010	0.001	0.012
run_query	0.000	0.000	0.001
sample_metadata	0.029	0.005	0.475
sample_region	0.000	0.001	0.001
save_query	0.053	0.006	0.838
select	0.067	0.008	0.058
semijoin	0.085	0.009	0.066
setdiff	0.067	0.008	0.069
show_dataset	0.062	0.015	11.122
show_jobs_list	0.043	0.002	0.362
show_queries_list	0.021	0.001	0.307
show_samples_list	0.022	0.000	0.330
show_schema	0.023	0.001	0.314
stop_gmql	0.204	0.067	0.102
stop_job	0	0	0
take	6.796	0.739	2.496
union	0.077	0.003	0.049
upload_dataset	0.001	0.000	0.000