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Trouble with R CMD check

4 messages · Shewcraft, Ryan, Duncan Murdoch

Shewcraft, Ryan
# 
Friends,

I changed one line of a package at the source level and then rebuilt it.
When I run R CMD check, I get an error:

installing R.css in C:/polsplineRS.Rcheck


---------- Making package polsplineRS ------------
  adding build stamp to DESCRIPTION
  making DLL ...
making hareall.d from hareall.c
making heftall.d from heftall.c
making lsdall.d from lsdall.c
making lspecall.d from lspecall.c
making nlsd.d from nlsd.c
making polyall.d from polyall.c
making polymars.d from polymars.c
gcc   -Ic:/PROGRA~1/R/R-24~1.1/include  -Wall -O2 -std=gnu99   -c
hareall.c -o hareall.o
hareall.c: In function `gremdim':
hareall.c:2127: warning: unused variable `x'
hareall.c: In function `compall':
hareall.c:1656: warning: 'lala' might be used uninitialized in this
function
hareall.c: In function `newton':
hareall.c:1876: warning: 'rall' might be used uninitialized in this
function
hareall.c: In function `search':
hareall.c:646: warning: 'iloc' might be used uninitialized in this
function
hareall.c:646: warning: 'lloc' might be used uninitialized in this
function
hareall.c:646: warning: 'uloc' might be used uninitialized in this
function
hareall.c: In function `adders':
hareall.c:529: warning: 'crit1' might be used uninitialized in this
function
hareall.c: In function `share':
hareall.c:2126: warning: 'bb1' might be used uninitialized in this
function
hareall.c:2126: warning: 'bt1' might be used uninitialized in this
function
hareall.c:2126: warning: 'bb2' might be used uninitialized in this
function
hareall.c:2126: warning: 'bw' might be used uninitialized in this
function
hareall.c:2127: warning: 'wald' might be used uninitialized in this
function
hareall.c: In function `sphare':
hareall.c:3417: warning: 's' might be used uninitialized in this
function
hareall.c: At top level:
hareall.c:132: warning: 'iigvector' declared `static' but never defined
gcc   -Ic:/PROGRA~1/R/R-24~1.1/include  -Wall -O2 -std=gnu99   -c
heftall.c -o heftall.o
heftall.c: In function `sheft':
heftall.c:301: warning: 'nintx' might be used uninitialized in this
function
heftall.c:301: warning: 'addi' might be used uninitialized in this
function
heftall.c:1848: warning: 'loloc' might be used uninitialized in this
function
heftall.c:1848: warning: 'uploc' might be used uninitialized in this
function
heftall.c:1848: warning: 'nowloc1' might be used uninitialized in this
function
gcc   -Ic:/PROGRA~1/R/R-24~1.1/include  -Wall -O2 -std=gnu99   -c
lsdall.c -o lsdall.o
lsdall.c: In function `knotplace':
lsdall.c:1890: warning: 'ia' might be used uninitialized in this
function
lsdall.c:1895: warning: 'u3' might be used uninitialized in this
function
lsdall.c:1895: warning: 'u4' might be used uninitialized in this
function
lsdall.c: In function `liter':
lsdall.c:369: warning: 'zerror' might be used uninitialized in this
function
lsdall.c:370: warning: 'newlikelihood' might be used uninitialized in
this function
lsdall.c: In function `logcensor':
lsdall.c:51: warning: 'xnknots' might be used uninitialized in this
function
lsdall.c:55: warning: 'xczheta' might be used uninitialized in this
function
lsdall.c: In function `pqlsd':
lsdall.c:2908: warning: 'j' might be used uninitialized in this function
lsdall.c: At top level:
lsdall.c:1458: warning: 'fun2' defined but not used
lsdall.c:1471: warning: 'fun48' defined but not used
gcc   -Ic:/PROGRA~1/R/R-24~1.1/include  -Wall -O2 -std=gnu99   -c
lspecall.c -o lspecall.o
lspecall.c: In function `tsadd':
lspecall.c:626: warning: 'b2' might be used uninitialized in this
function
gcc   -Ic:/PROGRA~1/R/R-24~1.1/include  -Wall -O2 -std=gnu99   -c nlsd.c
-o nlsd.o
nlsd.c: In function `ludcmp':
nlsd.c:695: warning: 'imax' might be used uninitialized in this function
nlsd.c: In function `setupspace':
nlsd.c:1717: warning: 'm' might be used uninitialized in this function
nlsd.c: In function `startspace':
nlsd.c:1838: warning: 'l' might be used uninitialized in this function
nlsd.c: In function `pompall':
nlsd.c:1158: warning: 'f' might be used uninitialized in this function
nlsd.c: In function `nlsd':
nlsd.c:747: warning: 'nowloc1' might be used uninitialized in this
function
nlsd.c:747: warning: 'loloc' might be used uninitialized in this
function
nlsd.c:747: warning: 'uploc' might be used uninitialized in this
function
gcc   -Ic:/PROGRA~1/R/R-24~1.1/include  -Wall -O2 -std=gnu99   -c
polyall.c -o polyall.o
polyall.c: In function `poly':
polyall.c:3121: warning: 'okd' might be used uninitialized in this
function
polyall.c:2777: warning: 'aj' might be used uninitialized in this
function
polyall.c:2777: warning: 'ak' might be used uninitialized in this
function
polyall.c:2777: warning: 'sj' might be used uninitialized in this
function
polyall.c:2777: warning: 'sk' might be used uninitialized in this
function
polyall.c:2777: warning: 'bbi' might be used uninitialized in this
function
polyall.c:2777: warning: 'bbj' might be used uninitialized in this
function
polyall.c:2777: warning: 'bbk' might be used uninitialized in this
function
polyall.c:2778: warning: 'baj' might be used uninitialized in this
function
polyall.c:2778: warning: 'bak' might be used uninitialized in this
function
polyall.c:2778: warning: 'bsj' might be used uninitialized in this
function
polyall.c:2778: warning: 'bsk' might be used uninitialized in this
function
polyall.c:395: warning: 'iloc' might be used uninitialized in this
function
polyall.c:395: warning: 'lloc' might be used uninitialized in this
function
polyall.c:395: warning: 'uloc' might be used uninitialized in this
function
polyall.c: In function `proj':
polyall.c:1794: warning: 'k' might be used uninitialized in this
function
polyall.c:1794: warning: 'k0' might be used uninitialized in this
function
polyall.c:1794: warning: 'k1' might be used uninitialized in this
function
polyall.c:1794: warning: 'k2' might be used uninitialized in this
function
polyall.c:1794: warning: 'k3' might be used uninitialized in this
function
polyall.c:1794: warning: 'k4' might be used uninitialized in this
function
polyall.c:1794: warning: 'k5' might be used uninitialized in this
function
polyall.c:1794: warning: 'k6' might be used uninitialized in this
function
polyall.c: In function `spoly':
polyall.c:945: warning: 'numbers' might be used uninitialized in this
function
polyall.c:946: warning: 'ranges' might be used uninitialized in this
function
polyall.c:948: warning: 'tdata' might be used uninitialized in this
function
polyall.c:948: warning: 'zdata' might be used uninitialized in this
function
polyall.c:949: warning: 'loss' might be used uninitialized in this
function
polyall.c:1575: warning: 'bestl' might be used uninitialized in this
function
polyall.c:1575: warning: 'bestu' might be used uninitialized in this
function
gcc   -Ic:/PROGRA~1/R/R-24~1.1/include  -Wall -O2 -std=gnu99   -c
polymars.c -o polymars.o
polymars.c: In function `fit_model':
polymars.c:513: warning: unused variable `intercept_sd'
polymars.c: In function `find_best_candidate':
polymars.c:1361: warning: unused variable `dok1'
polymars.c:1361: warning: unused variable `dok2'
polymars.c: In function `initial_model':
polymars.c:2585: warning: unused variable `mesh_index'
polymars.c: In function `lsame':
polymars.c:3925: warning: suggest parentheses around && within ||
polymars.c:3926: warning: suggest parentheses around && within ||
polymars.c:3929: warning: suggest parentheses around && within ||
polymars.c:3930: warning: suggest parentheses around && within ||
polymars.c: In function `dspmv':
polymars.c:4963: warning: suggest parentheses around && within ||
polymars.c: In function `condition':
polymars.c:6566: warning: unused variable `tt'
polymars.c: In function `fit_as_candidate':
polymars.c:1046: warning: 'knot1_value' might be used uninitialized in
this function
polymars.c:1046: warning: 'knot2_value' might be used uninitialized in
this function
polymars.c: In function `find_best_candidate':
polymars.c:1686: warning: 'current_predictor_values2' might be used
uninitialized in this function
polymars.c:1686: warning: 'knot1_value' might be used uninitialized in
this function
polymars.c:1686: warning: 'knot2_value' might be used uninitialized in
this function
polymars.c: In function `fit_model':
polymars.c:2164: warning: 'trailing_column' might be used uninitialized
in this function
polymars.c:2586: warning: 'knot_1_value' might be used uninitialized in
this function
polymars.c:2586: warning: 'knot_2_value' might be used uninitialized in
this function
polymars.c:2591: warning: 'means' might be used uninitialized in this
function
polymars.c:2591: warning: 'SDs' might be used uninitialized in this
function
polymars.c: In function `polymars':
polymars.c:358: warning: 'mesh' might be used uninitialized in this
function
polymars.c:6318: warning: 'mesh' might be used uninitialized in this
function
polymars.c:6318: warning: 'mesh' might be used uninitialized in this
function
g77 -O2 -Wall   -c allpack.f -o allpack.o
allpack.f: In subroutine `xdsidi':
In file included from allpack.f:0:
allpack.f:476: warning: 'ten' might be used uninitialized in this
function
windres --include-dir c:/PROGRA~1/R/R-24~1.1/include  -i
polsplineRS_res.rc -o polsplineRS_res.o
gcc  -shared -s  -o polsplineRS.dll polsplineRS.def hareall.o heftall.o
lsdall.o lspecall.o nlsd.o polyall.o polymars.o allpack.o
polsplineRS_res.o  -Lc:/PROGRA~1/R/R-24~1.1/bin
-Lc:/PROGRA~1/R/R-24~1.1/bin -lRblas -lg2c  -lg2c -lR
  ... DLL made
  installing DLL
  installing R files
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'polsplineRS'
     Formats: text html latex example chm 
  beta.polyclass                    text    html    latex   example chm
  clspec                            text    html    latex   example chm
  cpolyclass                        text    html    latex   example chm
  design.polymars                   text    html    latex   example chm
  dhare                             text    html    latex   example chm
  dheft                             text    html    latex   example chm
  dlogspline                        text    html    latex   example chm
  doldlogspline                     text    html    latex   example chm
  hare                              text    html    latex   example chm
  heft                              text    html    latex   example chm
  logspline                         text    html    latex   example chm
  lspec                             text    html    latex   example chm
  oldlogspline                      text    html    latex   example chm
  persp.polymars                    text    html    latex           chm
  plot.hare                         text    html    latex   example chm
  plot.heft                         text    html    latex   example chm
  plot.logspline                    text    html    latex   example chm
  plot.lspec                        text    html    latex   example chm
  plot.oldlogspline                 text    html    latex   example chm
  plot.polyclass                    text    html    latex   example chm
  plot.polymars                     text    html    latex   example chm
  polyclass                         text    html    latex   example chm
  polymars                          text    html    latex   example chm
  predict.polymars                  text    html    latex   example chm
  summary.hare                      text    html    latex   example chm
  summary.heft                      text    html    latex   example chm
  summary.logspline                 text    html    latex   example chm
  summary.lspec                     text    html    latex   example chm
  summary.oldlogspline              text    html    latex   example chm
  summary.polyclass                 text    html    latex   example chm
  summary.polymars                  text    html    latex   example chm
  testhare                          text    html    latex   example chm
  unstrip                           text    html    latex   example chm
  xhare                             text    html    latex           chm
hhc: not found
cp: cannot stat
`C:/polsplineRS.Rcheck/00_pkg_src/polsplineRS/chm/polsplineRS.chm': No
such file or directory
make[1]: *** [chm-polsplineRS] Error 1
make: *** [pkg-polsplineRS] Error 2
*** Installation of polsplineRS failed ***

Removing 'C:/polsplineRS.Rcheck/polsplineRS'

I am slowly figuring out all of this R stuff so I apologize for
continually bothering everyone.

Thanks,

Ryan Shewcraft
The Blackstone Group, L.P.
F: 646-253-7633 
 
--------------------------------------------------------

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Duncan Murdoch
#
On 3/7/2008 1:21 PM, Shewcraft, Ryan wrote:
You're getting lots of warnings from the compiler; presumably those have 
nothing to do with you.  Then at the end you're getting an error because 
you haven't set up your R toolset completely:

hhc: not found

This is the Microsoft Help Workshop help compiler.  Either you didn't 
install it, or didn't put it in the right place.  But you can avoid the 
error by just not building compiled help, using

Rcmd install --docs=normal polsplineRS

Duncan Murdoch
Shewcraft, Ryan
# 
Thanks!  That's seemed to partially work, but now when I try to load it
in R I get:

library(polsplineRS)
Error in library.dynam("polspline", pkg, lib) : 
        shared library 'polspline' not found
Error in library(polsplineRS) : .First.lib failed for 'polsplineRS' 

-----Original Message-----
From: Duncan Murdoch [mailto:murdoch at stats.uwo.ca] 
Sent: Friday, March 07, 2008 1:36 PM
To: Shewcraft, Ryan
Cc: r-help at r-project.org
Subject: Re: [R] Trouble with R CMD check
On 3/7/2008 1:21 PM, Shewcraft, Ryan wrote:
it.
You're getting lots of warnings from the compiler; presumably those have
nothing to do with you.  Then at the end you're getting an error because
you haven't set up your R toolset completely:

hhc: not found

This is the Microsoft Help Workshop help compiler.  Either you didn't
install it, or didn't put it in the right place.  But you can avoid the
error by just not building compiled help, using

Rcmd install --docs=normal polsplineRS

Duncan Murdoch
defined
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regarding this e-mail communication.
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Duncan Murdoch
#
On 3/7/2008 1:53 PM, Shewcraft, Ryan wrote:
Apparently you have renamed the package, but missed renaming it in the 
code in .First.lib.

Duncan Murdoch