Clear rchk messages on CRAN #3033

mattdowle · 2018-09-05T21:25:51Z

Current rchk messages on CRAN reproduced locally.

Package data.table version 1.11.4
Package built using 74847/R 3.6.0; x86_64-pc-linux-gnu; 2018-06-05 10:41:32 UTC; unix   
Checked with rchk version b882e37fb462917a8ab94e70394f3a797250b4e1
More information at https://github.com/kalibera/cran-checks/blob/master/rchk/PROTECT.md

Function chmatch2_old
[UP] calling allocating function unlist2(V) with a fresh pointer (l <arg 1>) data.table/src/rbindlist.c:825
Function fmelt [UP] unprotected variable dtnames while calling allocating function Rf_allocVector data.table/src/fmelt.c:663
[UP] unprotected variable dtnames while calling allocating function preprocess(?,?,?,V,V,?,?,?) data.table/src/fmelt.c:664
[UP] allocating function getvaluecols may destroy its unprotected argument (dtnames <arg 2>), which is later used. data.table/src/fmelt.c:670
[UP] calling allocating function getvaluecols with a fresh pointer (dtnames <arg 2>) data.table/src/fmelt.c:670
[UP] allocating function getvarcols may destroy its unprotected argument (dtnames <arg 2>), which is later used. data.table/src/fmelt.c:671
[UP] calling allocating function getvarcols with a fresh pointer (dtnames <arg 2>) data.table/src/fmelt.c:671
[UP] allocating function getidcols may destroy its unprotected argument (dtnames <arg 2>), which is later used. data.table/src/fmelt.c:672
[UP] unprotected variable dtnames while calling allocating function Rf_allocVector data.table/src/fmelt.c:675
[UP] unprotected variable dtnames while calling allocating function Rf_allocVector data.table/src/fmelt.c:684
Function gmax
[UP] calling allocating function Rf_coerceVector(V,?) with a fresh pointer (ans <arg 1>) data.table/src/gsumm.c:391
Function gmin
[UP] calling allocating function Rf_coerceVector(V,?) with a fresh pointer (ans <arg 1>) data.table/src/gsumm.c:260
Function reorder
[PB] has possible protection stack imbalance data.table/src/reorder.c:109
Function setselfref
[UP] calling allocating function R_MakeExternalPtr with argument allocated using Rf_getAttrib(?,S:names) data.table/src/assign.c:36
Function userOverride
[UP] calling allocating function chmatch(?,V,?,?) with argument allocated using Rf_getAttrib(?,S:names) data.table/src/freadR.c:227

codecov · 2018-09-05T21:52:21Z

Codecov Report

Merging #3033 into master will increase coverage by 0.01%.
The diff coverage is 75%.

@@            Coverage Diff             @@
##           master    #3033      +/-   ##
==========================================
+ Coverage   90.85%   90.87%   +0.01%     
==========================================
  Files          61       61              
  Lines       11736    11733       -3     
==========================================
- Hits        10663    10662       -1     
+ Misses       1073     1071       -2

Impacted Files	Coverage Δ
src/rbindlist.c	`89.27% <0%> (+0.34%)`	⬆️
src/freadR.c	`89.47% <100%> (ø)`	⬆️
src/reorder.c	`97.7% <100%> (ø)`	⬆️
src/gsumm.c	`87.86% <100%> (ø)`	⬆️
src/assign.c	`94.39% <100%> (ø)`	⬆️
src/fmelt.c	`84.71% <100%> (-0.04%)`	⬇️

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mattdowle · 2018-09-05T23:41:18Z

Local results of rchk now look good, iiuc. These remaining messages :
too many states
protect stack is too deep ... incomplete
relate to the rchk tool's limit and not that the actual stack is too deep, iiuc. They are filtered out by cran-checks I believe.

$ cat packages/lib/data.table/libs/*check
ERROR: too many states (abstraction error?) in function assign
ERROR: too many states (abstraction error?) in function dogroups
ERROR: too many states (abstraction error?) in function freadMain
ERROR: too many states (abstraction error?) in function assign
ERROR: too many states (abstraction error?) in function dogroups

Function assign
  [UP] protect stack is too deep, unprotecting all variables, results will be incomplete
  [UP] unprotected variable names while calling allocating function Rf_any_duplicated /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/assign.c:376
  [UP] unprotected variable names while calling allocating function Rf_coerceVector /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/assign.c:598
  [UP] unprotected variable names while calling allocating function Rf_type2char /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/assign.c:600
  [UP] unprotected variable names while calling allocating function Rf_type2char /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/assign.c:601
  [UP] unprotected variable names while calling allocating function Rf_warning /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/assign.c:620
  [UP] unprotected variable names while calling allocating function memrecycle /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/assign.c:628
  [UP] unprotected variable names while calling allocating function Rf_allocVector /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/assign.c:630
  [UP] calling allocating function chmatch(V,V,?,?) with argument allocated using Rf_mkString /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/assign.c:727
  [UP] unsupported form of unprotect, unprotecting all variables, results will be incomplete /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/assign.c:792

Function dogroups
  [UP] protect stack is too deep, unprotecting all variables, results will be incomplete
  [UP] protect stack is too deep, unprotecting all variables, results will be incomplete
  [UP] unprotected variable names while calling allocating function Rprintf /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/dogroups.c:373
  [UP] unprotected variable names while calling allocating function Rf_allocVector /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/dogroups.c:375
  [UP] unsupported form of unprotect, unprotecting all variables, results will be incomplete /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/dogroups.c:464

Function forder
  [UP] protect stack is too deep, unprotecting all variables, results will be incomplete
  [UP] protect stack is too deep, unprotecting all variables, results will be incomplete
  [UP] unsupported form of unprotect, unprotecting all variables, results will be incomplete /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/forder.c:1363

Function measurelist
  [UP] protect stack is too deep, unprotecting all variables, results will be incomplete
  [UP] unsupported form of unprotect, unprotecting all variables, results will be incomplete /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/fmelt.c:143

Function preprocess.769
  [PB] has too high protection stack depth results will be incomplete
  [UP] protect stack is too deep, unprotecting all variables, results will be incomplete
  [UP] unprotected variable col_name while calling allocating function Rf_allocVector /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/rbindlist.c:526
  [PB] has possible protection stack imbalance /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/rbindlist.c:589

Function rbindlist
  [PB] has an unsupported form of unprotect with a variable results will be incomplete /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/rbindlist.c:633
  [UP] unsupported form of unprotect, unprotecting all variables, results will be incomplete /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/rbindlist.c:633
  [UP] unprotected variable lnames while calling allocating function Rf_allocVector /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/rbindlist.c:774
  [PB] has an unsupported form of unprotect with a variable results will be incomplete /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/rbindlist.c:782
  [UP] unsupported form of unprotect, unprotecting all variables, results will be incomplete /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/rbindlist.c:782

Function shift
  [UP] protect stack is too deep, unprotecting all variables, results will be incomplete
  [UP] protect stack is too deep, unprotecting all variables, results will be incomplete
  [UP] unsupported form of unprotect, unprotecting all variables, results will be incomplete /home/mdowle/build/rchk/trunk/packages/build/TC1THj1Z/data.table/src/shift.c:214
Analyzed 245 functions, traversed 6373563 states.

…ts, #3033. This NEWS item is live on GitHub and will reflect on CRAN in the next release. Realized missing news item as a result of tweeting thanks: https://twitter.com/MattDowle/status/1042835186801471488

Too early UNPROTECT in rbindlist.c. Thanks to rchk.

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4d39f52

mattdowle added this to the 1.11.6 milestone Sep 5, 2018

mattdowle changed the title ~~Too early UNPROTECT in rbindlist.c. Thanks to rchk.~~ Clear rchk messages on CRAN Sep 5, 2018

2nd attempt. Running rchk locally found it.

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923b71a

mattdowle added 5 commits Sep 5, 2018

rchk fmelt.c

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6394284

rchk gsumm.c

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fec67db

missing UNPROTECT in reorder.c

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68bdcaf

rchk setselfref in assign.c

7b69545

rchk getAttrib in freadR.c

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8bef1a0

mattdowle merged commit a500a5a into master Sep 5, 2018
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mattdowle deleted the rchk branch Sep 5, 2018

mattdowle mentioned this pull request Sep 20, 2018

rchk messages 1.11.4 #2916

Closed

Rdatatable / data.table

Clear rchk messages on CRAN #3033

Clear rchk messages on CRAN #3033

mattdowle commented Sep 5, 2018 •

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Rdatatable / data.table

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Clear rchk messages on CRAN #3033

Clear rchk messages on CRAN #3033

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