Re: [R] Trouble with R CMD check

From: Duncan Murdoch <murdoch_at_stats.uwo.ca>
Date: Fri, 07 Mar 2008 13:36:22 -0500

On 3/7/2008 1:21 PM, Shewcraft, Ryan wrote:
> 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:

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

>
> 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.

>> 345 Park Avenue, 28th Floor
>> New York, NY 10154
>> P: 212-583-5147

> F: 646-253-7633
>
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R-help_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Fri 07 Mar 2008 - 18:37:57 GMT

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