* using log directory 'd:/Rcompile/CRANpkg/local/3.6/magmaR.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'magmaR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'magmaR' version '1.0.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'dittoSeq'
* 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 whether package 'magmaR' can be installed ... OK
* checking installed package size ... OK
* 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 loading without being on the library search path ... 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 ... [4s] 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [1s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [9s] ERROR
  Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > test_check("magmaR")
  Loading required package: magmaR
  == Failed tests ================================================================
  -- Error (test-matrix.R:14:9): retrieveMatrix ----------------------------------
  Error: subscript out of bounds
  Backtrace:
      x
   1. \-magmaR::retrieveMatrix(targ, "example", "rna_seq", attributeNames = "gene_counts") test-matrix.R:14:8
   2.   \-base::lapply(...)
   3.     \-magmaR:::FUN(X[[i]], ...)
   4.       \-magmaR:::.matrix_retrieval_chunk(...)
   5.         \-base::lapply(...)
   6.           \-magmaR:::FUN(X[[i]], ...)
  -- Failure (test-matrix.R:41:9): retrieveMatrix warns but ignores empty records --
  `mat` has type 'logical', not 'integer'.
  -- Failure (test-matrix.R:42:9): retrieveMatrix warns but ignores empty records --
  dim(mat) not equal to c(40, 12).
  2/2 mismatches (average diff: 26)
  [1] 0 - 40 == -40
  [2] 0 - 12 == -12
  -- Failure (test-special.R:26:3): retrieveIds ----------------------------------
  `ret` has type 'integer', not 'character'.
  -- Error (test-update.R:10:1): (code run outside of `test_that()`) -------------
  Error: subscript out of bounds
  Backtrace:
      x
   1. +-vcr::use_cassette(...) test-update.R:10:0
   2. | \-cassette$call_block(...)
   3. \-magmaR::retrieveMatrix(targ, "example", "rna_seq", "all", "gene_counts") test-update.R:11:4
   4.   \-base::lapply(...)
   5.     \-magmaR:::FUN(X[[i]], ...)
   6.       \-magmaR:::.matrix_retrieval_chunk(...)
   7.         \-base::lapply(...)
   8.           \-magmaR:::FUN(X[[i]], ...)
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 29 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [3s] WARNING
Error(s) in re-building vignettes:
--- re-building 'Download.Rmd' using rmarkdown
Quitting from lines 18-31 (Download.Rmd) 
Error: processing vignette 'Download.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'Download.Rmd'

--- re-building 'Upload.Rmd' using rmarkdown
Quitting from lines 18-31 (Upload.Rmd) 
Error: processing vignette 'Upload.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'Upload.Rmd'

SUMMARY: processing the following files failed:
  'Download.Rmd' 'Upload.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE