My package did not pass CRAN check due to error with test file using testthat. How can I fix this?

Ayala Allon

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Sep 22, 2016, 4:20:22 PM9/22/16

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Hey everyone,

I submitted my package to CRAN (this is not the first submission for this package) and it did not pass the CRAN check. This is the error they get and I have no idea how to fix it:

* checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Type 'contributors()' for more information and
  'citation()' on how to cite R or R packages in publications.

  Type 'demo()' for some demos, 'help()' for on-line help, or
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.

  > library(testthat)
  > library(prepdat)
  >
  > test_check("prepdat")
  Error: On CRAN
  testthat results     ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted

and this is how my test file looks (note that I used skip_on_cran; and here is a link to the test file on GitHub )

skip_on_cran()
library(prepdat)
data("finalized_stroopdata")
data("stroopdata")

context("Finalized table")

test_finalized_stroopdata <- prep(
  dataset = stroopdata
  , file_name = NULL
  , file_path = NULL
  , id = "subject"
  , within_vars = c("block", "target_type")
  , between_vars = c("order")
  , dvc = "rt"
  , dvd = "ac"
  , keep_trials = NULL
  , drop_vars = c()
  , keep_trials_dvc = "raw_data$rt > 100 & raw_data$rt < 3000 & raw_data$ac     == 1"
  , keep_trials_dvd = "raw_data$rt > 100 & raw_data$rt < 3000"
  , id_properties = c()
  , sd_criterion = c(1, 1.5, 2)
  , percentiles = c(0.05, 0.25, 0.75, 0.95)
  , outlier_removal = 2
  , keep_trials_outlier = "raw_data$ac == 1"
  , decimal_places = 0
  , notification = TRUE
  , dm = c()
  , save_results = FALSE
  , results_name = "results.txt"
  , results_path = NULL
  , save_summary = FALSE
)

test_that("Finialized table is correct", {
  expect_equal(test_finalized_stroopdata, finalized_stroopdata)
})

How can I fix this?

When I run devtools::check(document = FALSE) it goes without any errors, warnings, or notes.

Also, when I run devtools::test() (see below) the test goes without problems. I have no idea what can be the problem except that maybe for some reason the skip_on_cran() does not work.

Any help will be very much appreciated (also posted this question on Stackoverflow Stackoverflow),

Thank you,

Ayala

> test()

Loading prepdat

Testing prepdat

Finalized table:

raw_data has 5400 observations and 10 variables

subject block age gender order font_size trial_num target_type rt ac

1 5020 1 24 2 1 12 1 1 677 1

2 5020 1 24 2 1 12 2 1 538 1

3 5020 1 24 2 1 12 3 1 507 1

4 5020 1 24 2 1 12 4 1 2818 1

5 5020 1 24 2 1 12 5 1 582 1

6 5020 1 24 2 1 12 6 1 498 1

Found 1 between-subjects independent variable: order

Calculating between-subjects independent variables

Giving names for between-subjects variables

Finished between-subjects independent variables

Found 2 within-subject independent variables

within_condition column was added to raw_data

subject block age gender order font_size trial_num target_type rt ac

1 5020 1 24 2 1 12 1 1 677 1

2 5020 1 24 2 1 12 2 1 538 1

3 5020 1 24 2 1 12 3 1 507 1

4 5020 1 24 2 1 12 4 1 2818 1

5 5020 1 24 2 1 12 5 1 582 1

6 5020 1 24 2 1 12 6 1 498 1

within_condition

1 1_1

2 1_1

3 1_1

4 1_1

5 1_1

6 1_1

Finished within_condition column

Found dvc data

Creating data frame named raw_data_dvc for dvc data

Keeping trials according to keep_trials_dvc and deleting unnecessary trials in raw_data_dvc

All further calculations on dvc except outlier removal procedures will be done on the remaining trials

raw_data_dvc has 5260 observations and 11 variables

subject block age gender order font_size trial_num target_type rt ac

1 5020 1 24 2 1 12 1 1 677 1

2 5020 1 24 2 1 12 2 1 538 1

3 5020 1 24 2 1 12 3 1 507 1

4 5020 1 24 2 1 12 4 1 2818 1

5 5020 1 24 2 1 12 5 1 582 1

6 5020 1 24 2 1 12 6 1 498 1

within_condition

1 1_1

2 1_1

3 1_1

4 1_1

5 1_1

6 1_1

Found dvd data

Creating data frame named raw_data_dvd for dvd data

Keeping trials according to keep_trials_dvd and deleting unnecessary trials in raw_data_dvd

All further calculations on dvd will be done on the remaining trials

raw_data_dvd has 5356 observations and 11 variables

subject block age gender order font_size trial_num target_type rt ac

1 5020 1 24 2 1 12 1 1 677 1

2 5020 1 24 2 1 12 2 1 538 1

3 5020 1 24 2 1 12 3 1 507 1

4 5020 1 24 2 1 12 4 1 2818 1

5 5020 1 24 2 1 12 5 1 582 1

6 5020 1 24 2 1 12 6 1 498 1

within_condition

1 1_1

2 1_1

3 1_1

4 1_1

5 1_1

6 1_1

Your design is a mixed design (i.e., includes both between-subjects and within-subjects independent variables

Calculating mean dvc by id by within_condition

Calculating SD for dvc by id by within_condition using denominator n

Calculating median dvc by id by within_condition

Calculating mean dvc by id by within_condition after rejecting values above 1 SD

Calculating mean dvc by id by within_condition after rejecting values above 1.5 SD

Calculating mean dvc by id by within_condition after rejecting values above 2 SD

Counting number of rejected values for 1 SD

Counting number of rejected values for 1.5 SD

Counting number of rejected values for 2 SD

Counting number of values for dvc by id by within_condition before rejecting values according to sd_criterion

Calculating proportion of rejected values for dvc by id by within_condition for 1 SD

Calculating proportion of rejected values for dvc by id by within_condition for 1.5 SD

Calculating proportion of rejected values for dvc by id by within_condition for 2 SD

Calculating harmonic mean for dvc by id by condition

Calculating the 0.05 percentail for dvc by id by within_condition

Calculating the 0.25 percentail for dvc by id by within_condition

Calculating the 0.75 percentail for dvc by id by within_condition

Calculating the 0.95 percentail for dvc by id by within_condition

Keeping trials according to keep_trials_outlier and deleting unnecessary trials in raw_data

Outlier removal procedure will be calculated on the remaining trials

Calculating mean dvc by id by within_condition according to selected outlier removal procedure

Finished calculating means for dvc by id by within_condition according to modified-recursive procedure with moving criterion

Finished calculating dependent measures for dvc

Calculating mean dvd by id by within_condition

Calculating mean error by id by within_condition

Finished calculating dvd data

Creating results

Printing head results

subject order mdvc1 mdvc2 mdvc3 mdvc4 sdvc1 sdvc2 sdvc3 sdvc4

5013 5013 2 863 1038 1081 1103 328 214 417 321

5020 5020 1 707 781 637 713 410 362 305 328

5021 5021 2 655 742 559 653 162 170 121 144

5022 5022 1 604 725 580 650 108 153 128 135

5023 5023 2 747 827 909 963 265 200 347 243

5024 5024 1 616 793 667 764 125 157 182 180

meddvc1 meddvc2 meddvc3 meddvc4 t1dvc1 t1dvc2 t1dvc3 t1dvc4 t1.5dvc1

5013 758 1036 1014 1037 777 1047 1033 1065 790

5020 586 701 540 630 595 699 566 628 595

5021 633 780 540 630 632 760 536 625 630

5022 594 682 565 635 589 692 573 639 599

5023 726 834 821 900 724 825 858 923 718

5024 600 781 629 719 591 776 619 735 585

t1.5dvc2 t1.5dvc3 t1.5dvc4 t2dvc1 t2dvc2 t2dvc3 t2dvc4 n1tr1 n1tr2

5013 1013 1037 1054 809 1006 1001 1067 26 9

5020 699 566 626 595 699 566 632 11 2

5021 748 558 620 636 732 564 630 40 12

5022 698 569 627 602 725 563 638 25 11

5023 851 843 914 709 827 864 933 19 11

5024 756 619 745 591 756 635 751 30 9

n1tr3 n1tr4 n1.5tr1 n1.5tr2 n1.5tr3 n1.5tr4 n2tr1 n2tr2 n2tr3 n2tr4

5013 6 29 13 5 4 13 7 2 2 8

5020 2 12 11 2 2 11 11 2 2 10

5021 7 34 18 5 3 12 8 1 2 7

5022 5 44 12 7 2 17 6 0 1 7

5023 6 31 8 6 2 17 5 2 1 8

5024 5 21 15 3 5 7 10 3 2 4

ndvc1 ndvc2 ndvc3 ndvc4 p1tr1 p1tr2 p1tr3 p1tr4 p1.5tr1 p1.5tr2

5013 144 36 36 143 0.181 0.250 0.167 0.203 0.090 0.139

5020 143 35 36 142 0.077 0.057 0.056 0.085 0.077 0.057

5021 143 34 36 140 0.280 0.353 0.194 0.243 0.126 0.147

5022 143 34 36 144 0.175 0.324 0.139 0.306 0.084 0.206

5023 143 34 35 142 0.133 0.324 0.171 0.218 0.056 0.176

5024 144 35 36 143 0.208 0.257 0.139 0.147 0.104 0.086

p1.5tr3 p1.5tr4 p2tr1 p2tr2 p2tr3 p2tr4 rminv1 rminv2 rminv3 rminv4

5013 0.111 0.091 0.049 0.056 0.056 0.056 777 997 951 1019

5020 0.056 0.077 0.077 0.057 0.056 0.070 612 710 575 648

5021 0.083 0.086 0.056 0.029 0.056 0.050 617 701 501 626

5022 0.056 0.118 0.042 0.000 0.028 0.049 586 694 559 623

5023 0.057 0.120 0.035 0.059 0.029 0.056 685 773 823 908

5024 0.139 0.049 0.069 0.086 0.056 0.028 596 767 630 732

p0.05dvc1 p0.05dvc2 p0.05dvc3 p0.05dvc4 p0.25dvc1 p0.25dvc2

5013 539 744 575 704 666 890

5020 474 532 454 506 515 639

5021 447 485 457 484 552 595

5022 498 507 437 461 548 608

5023 433 482 549 668 641 722

5024 484 595 496 585 536 704

p0.25dvc3 p0.25dvc4 p0.75dvc1 p0.75dvc2 p0.75dvc3 p0.75dvc4

5013 858 910 958 1150 1182 1245

5020 508 575 684 764 625 702

5021 502 550 735 866 607 699

5022 528 564 650 834 610 734

5023 706 794 820 953 1027 1096

5024 556 658 660 832 696 838

p0.95dvc1 p0.95dvc2 p0.95dvc3 p0.95dvc4 mdvd1 mdvd2 mdvd3 mdvd4

5013 1463 1440 1780 1649 1.000 1.000 1 0.993

5020 1857 1198 1035 1568 1.000 0.972 1 0.986

5021 959 990 744 941 1.000 0.944 1 0.972

5022 745 971 707 888 0.993 0.944 1 1.000

5023 1035 1140 1405 1439 1.000 0.944 1 0.986

5024 887 1120 1063 1027 1.000 0.972 1 1.000

merr1 merr2 merr3 merr4 mrmc1 mrmc2 mrmc3 mrmc4 pmrmc1 pmrmc2 pmrmc3

5013 0.000 0.000 0 0.007 809 1038 1001 1058 4.861 0.000 5.556

5020 0.000 0.028 0 0.014 589 699 566 626 9.722 5.714 5.556

5021 0.000 0.056 0 0.028 655 742 572 642 0.000 0.000 2.778

5022 0.007 0.056 0 0.000 604 725 563 650 2.098 0.000 2.778

5023 0.000 0.056 0 0.014 709 827 843 955 4.167 0.000 8.333

5024 0.000 0.028 0 0.000 609 777 611 751 1.389 2.857 11.111

pmrmc4 nmrmc1 nmrmc2 nmrmc3 nmrmc4 tmrmc1 tmrmc2 tmrmc3 tmrmc4

5013 4.196 7 0 2 6 144 36 36 143

5020 7.746 14 2 2 11 144 35 36 142

5021 2.143 0 0 1 3 143 34 36 140

5022 0.000 3 0 1 0 143 34 36 144

5023 0.704 6 0 3 1 144 34 36 142

5024 2.083 2 1 4 3 144 35 36 144

prep() returned a data frame to console

Hip Hip Hooray! prep() finished

Have a great day and may all your results be significant!

.

DONE =====================================================================

Tal Galili

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Sep 22, 2016, 4:27:40 PM9/22/16

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Hi Ayala,

What does it show when using

devtools::build_win()

?

(link?)

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Ayala Allon

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Sep 22, 2016, 4:32:48 PM9/22/16

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Hey Tal,

Thank you for answering so quickly. I really appreciate it.

Here is what I get:

> devtools::build_win()

Building windows version of prepdat for R-devel with win-builder.r-project.org.

Email results to ayala...@gmail.com?

1: Not yet

2: For sure

3: No way

Selection: 2

'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file \

--no-environ --no-save --no-restore --quiet CMD build \

'/Users/ayalaallon/Dropbox/R/prepdat' --no-resave-data --no-manual

* checking for file ‘/Users/ayalaallon/Dropbox/R/prepdat/DESCRIPTION’ ... OK

* preparing ‘prepdat’:

* checking DESCRIPTION meta-information ... OK

* checking for LF line-endings in source and make files

* checking for empty or unneeded directories

* looking to see if a ‘data/datalist’ file should be added

* building ‘prepdat_1.0.8.tar.gz’

Error in curl::curl_fetch_memory(url, handle = h) : Timeout was reached

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Ayala Allon, PhD Candidate

The Visual Working Memory Lab

School of Psychological Sciences

Tel-Aviv University

ayala...@gmail.com

Check out my new R package on CRAN and GitHub

http://people.socsci.tau.ac.il/mu/royluria/

Tal Galili

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Sep 22, 2016, 4:45:28 PM9/22/16

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mmm,

That sounds like another issue.

Try using this:

https://win-builder.r-project.org/upload.aspx

----------------Contact Details:-------------------------------------------------------
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Ayala Allon, PhD Candidate
The Visual Working Memory Lab
School of Psychological Sciences
Tel-Aviv University
ayala...@gmail.com
Check out my new R package on CRAN and GitHub
http://people.socsci.tau.ac.il/mu/royluria/

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Ayala Allon

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Sep 22, 2016, 4:49:49 PM9/22/16

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Thanks. However, I did check it under Windows and OS X before submission.

Ayala

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Tal Galili

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Sep 22, 2016, 4:53:38 PM9/22/16

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Yes, but there you can ask to check the R-devel version. It is comfortable, and external to your own system (Which is good).

----------------Contact Details:-------------------------------------------------------
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Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English)
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Ayala Allon

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Sep 22, 2016, 6:07:54 PM9/22/16

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Got it

Attach are the results for this check.

Any suggestions will be great!

Ayala

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00check.log.txt

win-builder.r-project.org - _xW1xOX306u7q_examples_and_tests_.htm

00install.out.txt

Tal Galili

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Sep 22, 2016, 6:16:51 PM9/22/16

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Odd.

In any case, the code for tests should be inside test_that. I created a pull request with a fix. I'm not sure it would solve the problem, but please try it and tell us if it helps.

Tal

----------------Contact Details:-------------------------------------------------------
Contact me: Tal.G...@gmail.com |
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Ayala Allon

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Sep 23, 2016, 2:18:52 AM9/23/16

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Fixed it according to your pull request.

Still getting the same error

https://win-builder.r-project.org/4aeY2xuzT67I/

It seems something gets wrong when trying to run

> library(testthat)
> library(prepdat)
> 
> test_check("prepdat")
Error: On CRAN
testthat results ================================================================
OK: 0 SKIPPED: 0 FAILED: 0
Execution halted

https://win-builder.r-project.org/4aeY2xuzT67I/examples_and_tests/tests_i386/testthat.Rout.fail

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Ayala Allon, PhD Candidate
The Visual Working Memory Lab
School of Psychological Sciences
Tel-Aviv University
ayala...@gmail.com
Check out my new R package on CRAN and GitHub
http://people.socsci.tau.ac.il/mu/royluria/

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Ayala Allon, PhD Candidate
The Visual Working Memory Lab
School of Psychological Sciences
Tel-Aviv University
ayala...@gmail.com
Check out my new R package on CRAN and GitHub
http://people.socsci.tau.ac.il/mu/royluria/

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Ayala Allon, PhD Candidate
The Visual Working Memory Lab
School of Psychological Sciences
Tel-Aviv University
ayala...@gmail.com
Check out my new R package on CRAN and GitHub
http://people.socsci.tau.ac.il/mu/royluria/

Ayala Allon

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Sep 23, 2016, 3:38:36 AM9/23/16

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Also, when I run testtaht::test_check() I get:

> test_check("prepdat")

Loading required package: prepdat

Error: No tests found for prepdat

Ayala Allon

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Sep 23, 2016, 4:34:24 AM9/23/16

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I think I'm toward of solving this.

Someone told me on Stackoverflow to move the skip_on_cran() inside the test block. I did it and then used https://win-builder.r-project.org/upload.aspx again.

This time I get https://win-builder.r-project.org/S7m87yL2xI2f/00check.log (see below).

Should I run more checks before submitting to CRAN again?

Thanks!

* using log directory 'd:/RCompile/CRANguest/R-release/prepdat.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'prepdat/DESCRIPTION' ... OK
* this is package 'prepdat' version '1.0.8'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Ayala S. Allon <ayala...@gmail.com>'

Possibly mis-spelled words in DESCRIPTION:
  ANOVA (10:4)
  Jolicoeur (30:52)
  Selst (30:44)
  dataset (19:68, 20:45)
  txt (33:50)
* 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 whether package 'prepdat' can be installed ... OK
* checking installed package size ... OK
* checking package 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking Rd files ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking examples ...
** running examples for arch 'i386' ... [1s] OK
** running examples for arch 'x64' ... [1s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ... [1s] OK
  Running 'testthat.R' [1s]
** running tests for arch 'x64' ... [1s] OK
  Running 'testthat.R' [1s]
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE

Tal Galili

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Sep 23, 2016, 4:50:29 AM9/23/16

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It looks good. See if any of your "mis-spelled" words could be placed inside parenthesis.

Cheers,

Tal

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Contact me: Tal.G...@gmail.com |
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Ayala Allon, PhD Candidate
The Visual Working Memory Lab
School of Psychological Sciences
Tel-Aviv University
ayala...@gmail.com
Check out my new R package on CRAN and GitHub
http://people.socsci.tau.ac.il/mu/royluria/

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Ayala Allon, PhD Candidate
The Visual Working Memory Lab
School of Psychological Sciences
Tel-Aviv University
ayala...@gmail.com
Check out my new R package on CRAN and GitHub
http://people.socsci.tau.ac.il/mu/royluria/

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Ayala Allon, PhD Candidate
The Visual Working Memory Lab
School of Psychological Sciences
Tel-Aviv University
ayala...@gmail.com
Check out my new R package on CRAN and GitHub
http://people.socsci.tau.ac.il/mu/royluria/

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Ayala Allon

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Sep 23, 2016, 4:53:45 AM9/23/16

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Thanks.

I had these "mis-spelled" words also in the DESCRIPTION file in previous versions and it passed so I'll take my chances.

I'll update once it is on CRAN.

Ayala

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Ayala Allon

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Sep 23, 2016, 4:09:20 PM9/23/16

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Package is on CRAN.

Thanks for the help Tal!

Ayala

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Ayala Allon, PhD Candidate
The Visual Working Memory Lab
School of Psychological Sciences
Tel-Aviv University
ayala...@gmail.com
Check out my new R package on CRAN and GitHub
http://people.socsci.tau.ac.il/mu/royluria/

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Ayala Allon, PhD Candidate
The Visual Working Memory Lab
School of Psychological Sciences
Tel-Aviv University
ayala...@gmail.com
Check out my new R package on CRAN and GitHub
http://people.socsci.tau.ac.il/mu/royluria/

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Ayala Allon, PhD Candidate
The Visual Working Memory Lab
School of Psychological Sciences
Tel-Aviv University
ayala...@gmail.com
Check out my new R package on CRAN and GitHub
http://people.socsci.tau.ac.il/mu/royluria/

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Tal Galili

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Sep 23, 2016, 4:11:38 PM9/23/16

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Good job Ayala :)

Sent from a smart-phone

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