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krlmlr
Appveyor takes more than one hour to check examples and stops there, resulting in appveyor build failure with a message "Build execution time has reached the maximum allowed time for your plan (60 minutes)". I have ran checks for examples on windows 10 machine successfully without any warnings. Can you point us the reason or solution?
Build started
2$ErrorActionPreference = "Stop"
3Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
4Import-Module '..\appveyor-tool.ps1'
5
6git clone -q --branch=master https://github.com/Mathelab/IntLIM.git C:\projects\intlim
7git checkout -qf b4e649d20e296fa7d0b5bfdf07bcc6973d2815a9
8Running Install scripts
9Bootstrap
10== 07/03/2019 10:29:24: Bootstrap: Start
11== 07/03/2019 10:29:24: Adding GnuWin32 tools to PATH
12== 07/03/2019 10:29:24: Setting time zone
13UTC
14GMT Standard Time
15== 07/03/2019 10:29:24: Version: release
16== 07/03/2019 10:29:28: URL path:
17== 07/03/2019 10:29:28: Downloading R from: https://cloud.r-project.org/bin/windows/base/R-3.6.0-win.exe
18== 07/03/2019 10:29:30: Running R installer
19R is now available on drive C:
20== 07/03/2019 10:29:46: Setting PATH
21== 07/03/2019 10:29:46: Testing R installation
22R version 3.6.0 (2019-04-26)
23Platform: x86_64-w64-mingw32/x64 (64-bit)
24Running under: Windows Server 2012 R2 x64 (build 9600)
25
26Matrix products: default
27
28locale:
29[1] LC_COLLATE=English_United States.1252
30[2] LC_CTYPE=English_United States.1252
31[3] LC_MONETARY=English_United States.1252
32[4] LC_NUMERIC=C
33[5] LC_TIME=English_United States.1252
34
35attached base packages:
36[1] stats graphics grDevices utils datasets methods base
37
38loaded via a namespace (and not attached):
39[1] compiler_3.6.0
40== 07/03/2019 10:29:46: Determining Rtools version
41== 07/03/2019 10:29:46: Downloading Rtools from: https://cloud.r-project.org/bin/windows/Rtools/Rtools35.exe
42== 07/03/2019 10:29:48: Running Rtools installer
43Rtools is now available on drive C:
44== 07/03/2019 10:30:30: Setting PATH
45== 07/03/2019 10:30:30: Downloading and installing travis-tool.sh
[email protected] ../travis-tool.sh %*
47^..Rproj$
48^.travis.yml$
49^.Rproj.user$
50^doc$
51^Meta$
52^travis-tool.sh.cmd$
53C:\Rtools\bin
54C:\Rtools\MinGW\bin
55C:\Rtools\gcc-4.6.3\bin
56C:\R\bin\x64
57C:\Rtools\mingw_64\bin
58C:\MinGW\msys\1.0\bin
59C:\Program Files (x86)\Git\bin
60C:\Program Files (x86)\Microsoft SDKs\Azure\CLI2\wbin
61C:\Perl\site\bin
62C:\Perl\bin
63C:\Windows\system32
64C:\Windows
65C:\Windows\System32\Wbem
66C:\Windows\System32\WindowsPowerShell\v1.0
67C:\Program Files\7-Zip
68C:\Program Files\Microsoft\Web Platform Installer
69C:\Tools\GitVersion
70C:\Tools\PsTools
71C:\Program Files\Git LFS
72C:\Program Files (x86)\Subversion\bin
73C:\Program Files\Microsoft SQL Server\120\Tools\Binn
74C:\Program Files\Microsoft SQL Server\Client SDK\ODBC\110\Tools\Binn
75C:\Program Files (x86)\Microsoft SQL Server\120\Tools\Binn
76C:\Program Files\Microsoft SQL Server\120\DTS\Binn
77C:\Program Files (x86)\Microsoft SQL Server\120\Tools\Binn\ManagementStudio
78C:\Tools\WebDriver
79C:\Program Files (x86)\Microsoft SDKs\TypeScript\1.4
80C:\Program Files (x86)\Microsoft Visual Studio 12.0\Common7\IDE\PrivateAssemblies
81C:\Program Files (x86)\Microsoft SDKs\Azure\CLI\wbin
82C:\Ruby193\bin
83C:\Tools\NUnit\bin
84C:\Tools\xUnit
85C:\Tools\MSpec
86C:\Tools\Coverity\bin
87C:\Program Files (x86)\CMake\bin
88C:\go\bin
89C:\Program Files\Java\jdk1.8.0\bin
90C:\Python27
91C:\Program Files\nodejs
92C:\Program Files (x86)\iojs
93C:\Program Files\iojs
94C:\Program Files\Microsoft SQL Server\130\Tools\Binn
95C:\Program Files (x86)\MSBuild\14.0\Bin
96C:\Tools\NuGet
97C:\Program Files (x86)\Microsoft Visual Studio 14.0\Common7\IDE\CommonExtensions\Microsoft\TestWindow
98C:\Program Files\Microsoft DNX\Dnvm
99C:\Program Files\Microsoft SQL Server\Client SDK\ODBC\130\Tools\Binn
100C:\Program Files (x86)\Microsoft SQL Server\130\Tools\Binn
101C:\Program Files (x86)\Microsoft SQL Server\130\DTS\Binn
102C:\Program Files\Microsoft SQL Server\130\DTS\Binn
103C:\Program Files (x86)\Microsoft SQL Server\110\DTS\Binn
104C:\Program Files (x86)\Microsoft SQL Server\120\DTS\Binn
105C:\Program Files (x86)\Apache\Maven\bin
106C:\Python27\Scripts
107C:\Tools\NUnit3
108C:\Program Files\Mercurial
109C:\Program Files\dotnet
110C:\Tools\curl\bin
111C:\Program Files\Amazon\AWSCLI
112C:\Program Files (x86)\Microsoft SQL Server\140\DTS\Binn
113C:\Program Files (x86)\Microsoft Visual Studio 14.0\Common7\IDE\Extensions\Microsoft\SQLDB\DAC\140
114C:\Tools\vcpkg
115C:\Program Files (x86)\Microsoft SQL Server\140\Tools\Binn
116C:\Program Files\Microsoft SQL Server\140\Tools\Binn
117C:\Program Files\Microsoft SQL Server\140\DTS\Binn
118C:\Program Files\erl9.2\bin
119C:\Program Files (x86)\NSIS
120C:\Tools\Octopus
121C:\Program Files\Git\cmd
122C:\Program Files\Git\usr\bin
123C:\Program Files\Microsoft Service Fabric\bin\Fabric\Fabric.Code
124C:\Program Files\Microsoft SDKs\Service Fabric\Tools\ServiceFabricLocalClusterManager
125C:\Program Files\LLVM\bin
126C:\Program Files (x86)\Yarn\bin
127C:\Users\appveyor\AppData\Roaming\npm
128C:\Program Files\PowerShell\6
129C:\ProgramData\chocolatey\bin
130C:\Program Files (x86)\nodejs
131C:\Users\appveyor.dotnet\tools
132C:\Users\appveyor\AppData\Local\Yarn\bin
133C:\Users\appveyor\AppData\Roaming\npm
134C:\Program Files\AppVeyor\BuildAgent
135== 07/03/2019 10:30:30: Setting R_LIBS_USER
136
137
138 Directory: C:
139
140
141Mode LastWriteTime Length Name
142---- ------------- ------ ----
143d----- 7/3/2019 10:30 AM RLibrary
144== 07/03/2019 10:30:30: Setting TAR to 'internal'
145== 07/03/2019 10:30:30: Bootstrap: Done
146
147
148travis-tool.sh install_bioc Biobase MultiDataSet BiocGenerics GenomicRanges IRanges
149+ CRAN=https://cran.rstudio.com
150+ BIOC=http://bioconductor.org/biocLite.R
151+ PKGTYPE=both
152+ BIOC_USE_DEVEL=FALSE
153++ uname -s
154+ OS=MSYS_NT-6.3-WOW
155+ PANDOC_VERSION=1.13.1
156+ PANDOC_DIR=/opt/pandoc
157+ PANDOC_URL=https://s3.amazonaws.com/rstudio-buildtools/pandoc-1.13.1.zip
158+ PATH='/c/Rtools/bin:/c/Rtools/MinGW/bin:/c/Rtools/gcc-4.6.3/bin:/c/R/bin/x64:/c/Rtools/mingw_64/bin:/usr/bin:/c/Program Files (x86)/Git/bin:/c/Program Files (x86)/Microsoft SDKs/Azure/CLI2/wbin:/c/Perl/site/bin:/c/Perl/bin:/c/Windows/system32:/c/Windows:/c/Windows/System32/Wbem:/c/Windows/System32/WindowsPowerShell/v1.0/:/c/Program Files/7-Zip:/c/Program Files/Microsoft/Web Platform Installer/:/c/Tools/GitVersion:/c/Tools/PsTools:/c/Program Files/Git LFS:/c/Program Files (x86)/Subversion/bin:/c/Program Files/Microsoft SQL Server/120/Tools/Binn/:/c/Program Files/Microsoft SQL Server/Client SDK/ODBC/110/Tools/Binn/:/c/Program Files (x86)/Microsoft SQL Server/120/Tools/Binn/:/c/Program Files/Microsoft SQL Server/120/DTS/Binn/:/c/Program Files (x86)/Microsoft SQL Server/120/Tools/Binn/ManagementStudio/:/c/Tools/WebDriver:/c/Program Files (x86)/Microsoft SDKs/TypeScript/1.4/:/c/Program Files (x86)/Microsoft Visual Studio 12.0/Common7/IDE/PrivateAssemblies/:/c/Program Files (x86)/Microsoft SDKs/Azure/CLI/wbin:/c/Ruby193/bin:/c/Tools/NUnit/bin:/c/Tools/xUnit:/c/Tools/MSpec:/c/Tools/Coverity/bin:/c/Program Files (x86)/CMake/bin:/c/go/bin:/c/Program Files/Java/jdk1.8.0/bin:/c/Python27:/c/Program Files/nodejs:/c/Program Files (x86)/iojs:/c/Program Files/iojs:/c/Program Files/Microsoft SQL Server/130/Tools/Binn/:/c/Program Files (x86)/MSBuild/14.0/Bin:/c/Tools/NuGet:/c/Program Files (x86)/Microsoft Visual Studio 14.0/Common7/IDE/CommonExtensions/Microsoft/TestWindow:/c/Program Files/Microsoft DNX/Dnvm:/c/Program Files/Microsoft SQL Server/Client SDK/ODBC/130/Tools/Binn/:/c/Program Files (x86)/Microsoft SQL Server/130/Tools/Binn/:/c/Program Files (x86)/Microsoft SQL Server/130/DTS/Binn/:/c/Program Files/Microsoft SQL Server/130/DTS/Binn/:/c/Program Files (x86)/Microsoft SQL Server/110/DTS/Binn/:/c/Program Files (x86)/Microsoft SQL Server/120/DTS/Binn/:/c/Program Files (x86)/Apache/Maven/bin:/c/Python27/Scripts:/c/Tools/NUnit3:/c/Program Files/Mercurial/:/c/Program Files/dotnet/:/c/Tools/curl/bin:/c/Program Files/Amazon/AWSCLI/:/c/Program Files (x86)/Microsoft SQL Server/140/DTS/Binn/:/c/Program Files (x86)/Microsoft Visual Studio 14.0/Common7/IDE/Extensions/Microsoft/SQLDB/DAC/140:/c/Tools/vcpkg:/c/Program Files (x86)/Microsoft SQL Server/140/Tools/Binn/:/c/Program Files/Microsoft SQL Server/140/Tools/Binn/:/c/Program Files/Microsoft SQL Server/140/DTS/Binn/:/c/Program Files/erl9.2/bin:/c/Program Files (x86)/NSIS:/c/Tools/Octopus:/c/Program Files/Git/cmd:/c/Program Files/Git/usr/bin:/c/Program Files/Microsoft Service Fabric/bin/Fabric/Fabric.Code:/c/Program Files/Microsoft SDKs/Service Fabric/Tools/ServiceFabricLocalClusterManager:/c/Program Files/LLVM/bin:/c/Program Files (x86)/Yarn/bin/:/c/Users/appveyor/AppData/Roaming/npm:/c/Program Files/PowerShell/6/:/c/ProgramData/chocolatey/bin:/c/Program Files (x86)/nodejs/:/c/Users/appveyor/.dotnet/tools:/c/Users/appveyor/AppData/Local/Yarn/bin:/c/Users/appveyor/AppData/Roaming/npm:/c/Program Files/AppVeyor/BuildAgent/:/usr/texbin'
159+ R_BUILD_ARGS=--no-manual
160+ R_CHECK_ARGS='--no-manual --as-cran'
161+ R_VERSION_TEST='getRversion() >= '''3.5.0''''
162+ R_USE_BIOC_INST='source('''http://bioconductor.org/biocLite.R'''); tryCatch(useDevel(FALSE), error=function(e) {if (!grepl('''already in use''', e)) {e}}); options(repos=biocinstallRepos())'
163+ R_USE_BIOC_MNGR='if (!requireNamespace('''BiocManager''', quietly=TRUE)) install.packages('''BiocManager''', repos=c(CRAN='''https://cran.rstudio.com''')); if (FALSE) BiocManager::install(version = '''devel'''); options(repos=BiocManager::repositories())'
164+ R_USE_BIOC_CMDS='if (getRversion() >= '''3.5.0''') {if (!requireNamespace('''BiocManager''', quietly=TRUE)) install.packages('''BiocManager''', repos=c(CRAN='''https://cran.rstudio.com''')); if (FALSE) BiocManager::install(version = '''devel'''); options(repos=BiocManager::repositories())} else {source('''http://bioconductor.org/biocLite.R'''); tryCatch(useDevel(FALSE), error=function(e) {if (!grepl('''already in use''', e)) {e}}); options(repos=biocinstallRepos())};'
165+ BIOC_INSTALL='{if (getRversion() >= '''3.5.0''') BiocManager::install else BiocInstaller::biocLite}'
166+ COMMAND=install_bioc
167+ echo 'Running command: install_bioc'
168Running command: install_bioc
169+ shift
170+ case $COMMAND in
171+ BiocInstall Biobase MultiDataSet BiocGenerics GenomicRanges IRanges
172+ [[ '' == \B\i\o\b\a\s\e\ \M\u\l\t\i\D\a\t\a\S\e\t\ \B\i\o\c\G\e\n\e\r\i\c\s\ \G\e\n\o\m\i\c\R\a\n\g\e\s\ \I\R\a\n\g\e\s ]]
173+ echo 'Installing R Bioconductor package(s): Biobase' MultiDataSet BiocGenerics GenomicRanges IRanges
174Installing R Bioconductor package(s): Biobase MultiDataSet BiocGenerics GenomicRanges IRanges
175+ Rscript -e 'if (getRversion() >= '''3.5.0''') {if (!requireNamespace('''BiocManager''', quietly=TRUE)) install.packages('''BiocManager''', repos=c(CRAN='''https://cran.rstudio.com''')); if (FALSE) BiocManager::install(version = '''devel'''); options(repos=BiocManager::repositories())} else {source('''http://bioconductor.org/biocLite.R'''); tryCatch(useDevel(FALSE), error=function(e) {if (!grepl('''already in use''', e)) {e}}); options(repos=biocinstallRepos())}; {if (getRversion() >= '''3.5.0''') BiocManager::install else BiocInstaller::biocLite}(commandArgs(TRUE))' Biobase MultiDataSet BiocGenerics GenomicRanges IRanges
176Installing package into 'c:/RLibrary'
177(as 'lib' is unspecified)
178trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/BiocManager_1.30.4.zip'
179Content type 'application/zip' length 292998 bytes (286 KB)
180==================================================
181downloaded 286 KB
182
183package 'BiocManager' successfully unpacked and MD5 sums checked
184
185The downloaded binary packages are in
186 C:\Users\appveyor\AppData\Local\Temp\1\RtmpEZn5pd\downloaded_packages
187Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
188Installing package(s) 'BiocVersion', 'Biobase', 'MultiDataSet', 'BiocGenerics',
189 'GenomicRanges', 'IRanges'
190also installing the dependencies 'formatR', 'lambda.r', 'futile.options', 'backports', 'zeallot', 'futile.logger', 'snow', 'BH', 'glue', 'magrittr', 'stringi', 'colorspace', 'assertthat', 'utf8', 'vctrs', 'matrixStats', 'BiocParallel', 'plyr', 'stringr', 'labeling', 'munsell', 'R6', 'RColorBrewer', 'cli', 'crayon', 'fansi', 'pillar', 'pkgconfig', 'bitops', 'DelayedArray', 'digest', 'gtable', 'lazyeval', 'reshape2', 'rlang', 'scales', 'tibble', 'viridisLite', 'withr', 'Rcpp', 'calibrate', 'RCurl', 'GenomeInfoDbData', 'zlibbioc', 'S4Vectors', 'SummarizedExperiment', 'ggplot2', 'ggrepel', 'qqman', 'limma', 'GenomeInfoDb', 'XVector'
191
192
193 There is a binary version available but the source version is later:
194 binary source needs_compilation
195BiocParallel 1.17.18 1.18.0 TRUE
196
197trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/formatR_1.7.zip'
198Content type 'application/zip' length 152430 bytes (148 KB)
199==================================================
200downloaded 148 KB
201
202trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/lambda.r_1.2.3.zip'
203Content type 'application/zip' length 112559 bytes (109 KB)
204==================================================
205downloaded 109 KB
206
207trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/futile.options_1.0.1.zip'
208Content type 'application/zip' length 21145 bytes (20 KB)
209==================================================
210downloaded 20 KB
211
212trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/backports_1.1.4.zip'
213Content type 'application/zip' length 66819 bytes (65 KB)
214==================================================
215downloaded 65 KB
216
217trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/zeallot_0.1.0.zip'
218Content type 'application/zip' length 62189 bytes (60 KB)
219==================================================
220downloaded 60 KB
221
222trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/futile.logger_1.4.3.zip'
223Content type 'application/zip' length 97464 bytes (95 KB)
224==================================================
225downloaded 95 KB
226
227trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/snow_0.4-3.zip'
228Content type 'application/zip' length 111094 bytes (108 KB)
229==================================================
230downloaded 108 KB
231
232trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/BH_1.69.0-1.zip'
233Content type 'application/zip' length 19008275 bytes (18.1 MB)
234==================================================
235downloaded 18.1 MB
236
237trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/glue_1.3.1.zip'
238Content type 'application/zip' length 172962 bytes (168 KB)
239==================================================
240downloaded 168 KB
241
242trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/magrittr_1.5.zip'
243Content type 'application/zip' length 158187 bytes (154 KB)
244==================================================
245downloaded 154 KB
246
247trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/stringi_1.4.3.zip'
248Content type 'application/zip' length 15297905 bytes (14.6 MB)
249==================================================
250downloaded 14.6 MB
251
252trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/colorspace_1.4-1.zip'
253Content type 'application/zip' length 2550405 bytes (2.4 MB)
254==================================================
255downloaded 2.4 MB
256
257trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/assertthat_0.2.1.zip'
258Content type 'application/zip' length 55132 bytes (53 KB)
259==================================================
260downloaded 53 KB
261
262trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/utf8_1.1.4.zip'
263Content type 'application/zip' length 215445 bytes (210 KB)
264==================================================
265downloaded 210 KB
266
267trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/vctrs_0.1.0.zip'
268Content type 'application/zip' length 621784 bytes (607 KB)
269==================================================
270downloaded 607 KB
271
272trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/matrixStats_0.54.0.zip'
273Content type 'application/zip' length 1636070 bytes (1.6 MB)
274==================================================
275downloaded 1.6 MB
276
277trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/plyr_1.8.4.zip'
278Content type 'application/zip' length 1302561 bytes (1.2 MB)
279==================================================
280downloaded 1.2 MB
281
282trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/stringr_1.4.0.zip'
283Content type 'application/zip' length 216597 bytes (211 KB)
284==================================================
285downloaded 211 KB
286
287trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/labeling_0.3.zip'
288Content type 'application/zip' length 62937 bytes (61 KB)
289==================================================
290downloaded 61 KB
291
292trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/munsell_0.5.0.zip'
293Content type 'application/zip' length 245256 bytes (239 KB)
294==================================================
295downloaded 239 KB
296
297trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/R6_2.4.0.zip'
298Content type 'application/zip' length 58832 bytes (57 KB)
299==================================================
300downloaded 57 KB
301
302trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/RColorBrewer_1.1-2.zip'
303Content type 'application/zip' length 55569 bytes (54 KB)
304==================================================
305downloaded 54 KB
306
307trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/cli_1.1.0.zip'
308Content type 'application/zip' length 176572 bytes (172 KB)
309==================================================
310downloaded 172 KB
311
312trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/crayon_1.3.4.zip'
313Content type 'application/zip' length 749351 bytes (731 KB)
314==================================================
315downloaded 731 KB
316
317trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/fansi_0.4.0.zip'
318Content type 'application/zip' length 221318 bytes (216 KB)
319==================================================
320downloaded 216 KB
321
322trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/pillar_1.4.2.zip'
323Content type 'application/zip' length 182635 bytes (178 KB)
324==================================================
325downloaded 178 KB
326
327trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/pkgconfig_2.0.2.zip'
328Content type 'application/zip' length 22316 bytes (21 KB)
329==================================================
330downloaded 21 KB
331
332trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/bitops_1.0-6.zip'
333Content type 'application/zip' length 38469 bytes (37 KB)
334==================================================
335downloaded 37 KB
336
337trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/DelayedArray_0.10.0.zip'
338Content type 'application/zip' length 2239865 bytes (2.1 MB)
339==================================================
340downloaded 2.1 MB
341
342trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/digest_0.6.19.zip'
343Content type 'application/zip' length 211452 bytes (206 KB)
344==================================================
345downloaded 206 KB
346
347trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/gtable_0.3.0.zip'
348Content type 'application/zip' length 434187 bytes (424 KB)
349==================================================
350downloaded 424 KB
351
352trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/lazyeval_0.2.2.zip'
353Content type 'application/zip' length 172261 bytes (168 KB)
354==================================================
355downloaded 168 KB
356
357trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/reshape2_1.4.3.zip'
358Content type 'application/zip' length 627773 bytes (613 KB)
359==================================================
360downloaded 613 KB
361
362trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/rlang_0.4.0.zip'
363Content type 'application/zip' length 1090280 bytes (1.0 MB)
364==================================================
365downloaded 1.0 MB
366
367trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/scales_1.0.0.zip'
368Content type 'application/zip' length 1071774 bytes (1.0 MB)
369==================================================
370downloaded 1.0 MB
371
372trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/tibble_2.1.3.zip'
373Content type 'application/zip' length 337182 bytes (329 KB)
374==================================================
375downloaded 329 KB
376
377trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/viridisLite_0.3.0.zip'
378Content type 'application/zip' length 60698 bytes (59 KB)
379==================================================
380downloaded 59 KB
381
382trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/withr_2.1.2.zip'
383Content type 'application/zip' length 152233 bytes (148 KB)
384==================================================
385downloaded 148 KB
386
387trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/Rcpp_1.0.1.zip'
388Content type 'application/zip' length 4495059 bytes (4.3 MB)
389==================================================
390downloaded 4.3 MB
391
392trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/calibrate_1.7.2.zip'
393Content type 'application/zip' length 326111 bytes (318 KB)
394==================================================
395downloaded 318 KB
396
397trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/RCurl_1.95-4.12.zip'
398Content type 'application/zip' length 2974210 bytes (2.8 MB)
399==================================================
400downloaded 2.8 MB
401
402trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/zlibbioc_1.30.0.zip'
403Content type 'application/zip' length 374970 bytes (366 KB)
404==================================================
405downloaded 366 KB
406
407trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/S4Vectors_0.22.0.zip'
408Content type 'application/zip' length 2030028 bytes (1.9 MB)
409==================================================
410downloaded 1.9 MB
411
412trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/SummarizedExperiment_1.14.0.zip'
413Content type 'application/zip' length 2806553 bytes (2.7 MB)
414==================================================
415downloaded 2.7 MB
416
417trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/ggplot2_3.2.0.zip'
418Content type 'application/zip' length 3964600 bytes (3.8 MB)
419==================================================
420downloaded 3.8 MB
421
422trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/ggrepel_0.8.1.zip'
423Content type 'application/zip' length 1133065 bytes (1.1 MB)
424==================================================
425downloaded 1.1 MB
426
427trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/qqman_0.1.4.zip'
428Content type 'application/zip' length 1415363 bytes (1.3 MB)
429==================================================
430downloaded 1.3 MB
431
432trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/limma_3.40.2.zip'
433Content type 'application/zip' length 3059804 bytes (2.9 MB)
434==================================================
435downloaded 2.9 MB
436
437trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/GenomeInfoDb_1.20.0.zip'
438Content type 'application/zip' length 3835294 bytes (3.7 MB)
439==================================================
440downloaded 3.7 MB
441
442trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/XVector_0.24.0.zip'
443Content type 'application/zip' length 714038 bytes (697 KB)
444==================================================
445downloaded 697 KB
446
447trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/BiocVersion_3.9.0.zip'
448Content type 'application/zip' length 8915 bytes
449==================================================
450downloaded 8915 bytes
451
452trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/Biobase_2.44.0.zip'
453Content type 'application/zip' length 2421976 bytes (2.3 MB)
454==================================================
455downloaded 2.3 MB
456
457trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/MultiDataSet_1.12.0.zip'
458Content type 'application/zip' length 1133701 bytes (1.1 MB)
459==================================================
460downloaded 1.1 MB
461
462trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/BiocGenerics_0.30.0.zip'
463Content type 'application/zip' length 736201 bytes (718 KB)
464==================================================
465downloaded 718 KB
466
467trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/GenomicRanges_1.36.0.zip'
468Content type 'application/zip' length 2135144 bytes (2.0 MB)
469==================================================
470downloaded 2.0 MB
471
472trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/IRanges_2.18.1.zip'
473Content type 'application/zip' length 2373684 bytes (2.3 MB)
474==================================================
475downloaded 2.3 MB
476
477package 'formatR' successfully unpacked and MD5 sums checked
478package 'lambda.r' successfully unpacked and MD5 sums checked
479package 'futile.options' successfully unpacked and MD5 sums checked
480package 'backports' successfully unpacked and MD5 sums checked
481package 'zeallot' successfully unpacked and MD5 sums checked
482package 'futile.logger' successfully unpacked and MD5 sums checked
483package 'snow' successfully unpacked and MD5 sums checked
484package 'BH' successfully unpacked and MD5 sums checked
485package 'glue' successfully unpacked and MD5 sums checked
486package 'magrittr' successfully unpacked and MD5 sums checked
487package 'stringi' successfully unpacked and MD5 sums checked
488package 'colorspace' successfully unpacked and MD5 sums checked
489package 'assertthat' successfully unpacked and MD5 sums checked
490package 'utf8' successfully unpacked and MD5 sums checked
491package 'vctrs' successfully unpacked and MD5 sums checked
492package 'matrixStats' successfully unpacked and MD5 sums checked
493package 'plyr' successfully unpacked and MD5 sums checked
494package 'stringr' successfully unpacked and MD5 sums checked
495package 'labeling' successfully unpacked and MD5 sums checked
496package 'munsell' successfully unpacked and MD5 sums checked
497package 'R6' successfully unpacked and MD5 sums checked
498package 'RColorBrewer' successfully unpacked and MD5 sums checked
499package 'cli' successfully unpacked and MD5 sums checked
500package 'crayon' successfully unpacked and MD5 sums checked
501package 'fansi' successfully unpacked and MD5 sums checked
502package 'pillar' successfully unpacked and MD5 sums checked
503package 'pkgconfig' successfully unpacked and MD5 sums checked
504package 'bitops' successfully unpacked and MD5 sums checked
505package 'DelayedArray' successfully unpacked and MD5 sums checked
506package 'digest' successfully unpacked and MD5 sums checked
507package 'gtable' successfully unpacked and MD5 sums checked
508package 'lazyeval' successfully unpacked and MD5 sums checked
509package 'reshape2' successfully unpacked and MD5 sums checked
510package 'rlang' successfully unpacked and MD5 sums checked
511package 'scales' successfully unpacked and MD5 sums checked
512package 'tibble' successfully unpacked and MD5 sums checked
513package 'viridisLite' successfully unpacked and MD5 sums checked
514package 'withr' successfully unpacked and MD5 sums checked
515package 'Rcpp' successfully unpacked and MD5 sums checked
516package 'calibrate' successfully unpacked and MD5 sums checked
517package 'RCurl' successfully unpacked and MD5 sums checked
518package 'zlibbioc' successfully unpacked and MD5 sums checked
519package 'S4Vectors' successfully unpacked and MD5 sums checked
520package 'SummarizedExperiment' successfully unpacked and MD5 sums checked
521package 'ggplot2' successfully unpacked and MD5 sums checked
522package 'ggrepel' successfully unpacked and MD5 sums checked
523package 'qqman' successfully unpacked and MD5 sums checked
524package 'limma' successfully unpacked and MD5 sums checked
525package 'GenomeInfoDb' successfully unpacked and MD5 sums checked
526package 'XVector' successfully unpacked and MD5 sums checked
527package 'BiocVersion' successfully unpacked and MD5 sums checked
528package 'Biobase' successfully unpacked and MD5 sums checked
529package 'MultiDataSet' successfully unpacked and MD5 sums checked
530package 'BiocGenerics' successfully unpacked and MD5 sums checked
531package 'GenomicRanges' successfully unpacked and MD5 sums checked
532package 'IRanges' successfully unpacked and MD5 sums checked
533
534The downloaded binary packages are in
535 C:\Users\appveyor\AppData\Local\Temp\1\RtmpEZn5pd\downloaded_packages
536installing the source packages 'BiocParallel', 'GenomeInfoDbData'
537
538trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/BiocParallel_1.18.0.tar.gz'
539Content type 'application/x-gzip' length 928675 bytes (906 KB)
540==================================================
541downloaded 906 KB
542
543trying URL 'https://bioconductor.org/packages/3.9/data/annotation/src/contrib/GenomeInfoDbData_1.2.1.tar.gz'
544Content type 'application/x-gzip' length 9792100 bytes (9.3 MB)
545==================================================
546downloaded 9.3 MB
547
548 installing source package 'BiocParallel' ...
549** using staged installation
550
551 **********************************************
552 WARNING: this package has a configure script
553 It probably needs manual configuration
554 **********************************************
555
556
557** libs
558
559*** arch - i386
560C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"c:/R/include" -DNDEBUG -I"c:/RLibrary/BH/include" -O2 -Wall -mtune=generic -c ipcmutex.cpp -o ipcmutex.o
561In file included from c:/RLibrary/BH/include/boost/random/detail/integer_log2.hpp:19:0,
562 from c:/RLibrary/BH/include/boost/random/detail/large_arithmetic.hpp:19,
563 from c:/RLibrary/BH/include/boost/random/detail/const_mod.hpp:23,
564 from c:/RLibrary/BH/include/boost/random/detail/seed_impl.hpp:26,
565 from c:/RLibrary/BH/include/boost/random/mersenne_twister.hpp:30,
566 from c:/RLibrary/BH/include/boost/uuid/random_generator.hpp:17,
567 from c:/RLibrary/BH/include/boost/uuid/uuid_generators.hpp:17,
568 from ipcmutex.cpp:3:
569c:/RLibrary/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
570 BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
571 ^
572In file included from c:/RLibrary/BH/include/boost/container/map.hpp:30:0,
573 from c:/RLibrary/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:37,
574 from c:/RLibrary/BH/include/boost/interprocess/mapped_region.hpp:50,
575 from c:/RLibrary/BH/include/boost/interprocess/detail/managed_open_or_create_impl.hpp:26,
576 from c:/RLibrary/BH/include/boost/interprocess/managed_shared_memory.hpp:26,
577 from ipcmutex.cpp:13:
578c:/RLibrary/BH/include/boost/container/detail/tree.hpp: In instantiation of 'T& boost::container::dtl::tree_node<T, VoidPointer, tree_type_value, OptimizeSize>::get_data() [with T = std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >; VoidPointer = void*; boost::container::tree_type_enum tree_type_value = (boost::container::tree_type_enum)0u; bool OptimizeSize = true]':
579c:/RLibrary/BH/include/boost/container/detail/iterators.hpp:854:36: required from 'boost::container::dtl::iterator_from_iiterator<IIterator, IsConst>::reference boost::container::dtl::iterator_from_iiterator<IIterator, IsConst>::operator*() const [with IIterator = boost::intrusive::tree_iterator<boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>; bool IsConst = false; boost::container::dtl::iterator_from_iiterator<IIterator, IsConst>::reference = std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >&]'
580c:/RLibrary/BH/include/boost/container/detail/iterators.hpp:857:87: required from 'boost::container::dtl::iterator_from_iiterator<IIterator, IsConst>::pointer boost::container::dtl::iterator_from_iiterator<IIterator, IsConst>::operator->() const [with IIterator = boost::intrusive::tree_iterator<boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>; bool IsConst = false; boost::container::dtl::iterator_from_iiterator<IIterator, IsConst>::pointer = std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >]'
581c:/RLibrary/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:220:41: required from here
582c:/RLibrary/BH/include/boost/container/detail/tree.hpp:148:56: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
583 { return reinterpret_cast<T>(this->m_storage.data); }
584 ^
585c:/RLibrary/BH/include/boost/container/detail/tree.hpp: In instantiation of 'T& boost::container::dtl::tree_node<T, VoidPointer, tree_type_value, OptimizeSize>::get_data() [with T = std::pair<const boost::container::basic_string<char, std::char_traits
702 BatchtoolsParam-class html
703 BiocParallel-package html
704 BiocParallelParam-class html
705 DeveloperInterface html
706 DoparParam-class html
707 MulticoreParam-class html
708 SerialParam-class html
709 SnowParam-class html
710 bpaggregate html
711 bpiterate html
712 bplapply html
713 bploop html
714 bpmapply html
715 bpok html
716 bpschedule html
717 bptry html
718 bpvalidate html
719 bpvec html
720 bpvectorize html
721 ipcmutex html
722 register html
723** building package indices
724** installing vignettes
725** testing if installed package can be loaded from temporary location
726*** arch - i386
727*** arch - x64
728** testing if installed package can be loaded from final location
729*** arch - i386
730*** arch - x64
731** testing if installed package keeps a record of temporary installation path
732* DONE (BiocParallel)
733* installing source package 'GenomeInfoDbData' ...
734** using staged installation
735** data
736** inst
737** help
738*** installing help indices
739 converting help for package 'GenomeInfoDbData'
740 finding HTML links ... done
741 GenomeInfoDbData-package html
742** building package indices
743** testing if installed package can be loaded from temporary location
744*** arch - i386
745*** arch - x64
746** testing if installed package can be loaded from final location
747*** arch - i386
748*** arch - x64
749** testing if installed package keeps a record of temporary installation path
750* DONE (GenomeInfoDbData)
751
752The downloaded source packages are in
753 'C:\Users\appveyor\AppData\Local\Temp\1\RtmpEZn5pd\downloaded_packages'
754Update old packages: 'cluster', 'nlme'
755travis-tool.sh install_deps
756+ CRAN=https://cran.rstudio.com
757+ BIOC=http://bioconductor.org/biocLite.R
758+ PKGTYPE=both
759+ BIOC_USE_DEVEL=FALSE
760++ uname -s
761+ OS=MSYS_NT-6.3-WOW
762+ PANDOC_VERSION=1.13.1
763+ PANDOC_DIR=/opt/pandoc
764+ PANDOC_URL=https://s3.amazonaws.com/rstudio-buildtools/pandoc-1.13.1.zip
765+ PATH='/c/Rtools/bin:/c/Rtools/MinGW/bin:/c/Rtools/gcc-4.6.3/bin:/c/R/bin/x64:/c/Rtools/mingw_64/bin:/usr/bin:/c/Program Files (x86)/Git/bin:/c/Program Files (x86)/Microsoft SDKs/Azure/CLI2/wbin:/c/Perl/site/bin:/c/Perl/bin:/c/Windows/system32:/c/Windows:/c/Windows/System32/Wbem:/c/Windows/System32/WindowsPowerShell/v1.0/:/c/Program Files/7-Zip:/c/Program Files/Microsoft/Web Platform Installer/:/c/Tools/GitVersion:/c/Tools/PsTools:/c/Program Files/Git LFS:/c/Program Files (x86)/Subversion/bin:/c/Program Files/Microsoft SQL Server/120/Tools/Binn/:/c/Program Files/Microsoft SQL Server/Client SDK/ODBC/110/Tools/Binn/:/c/Program Files (x86)/Microsoft SQL Server/120/Tools/Binn/:/c/Program Files/Microsoft SQL Server/120/DTS/Binn/:/c/Program Files (x86)/Microsoft SQL Server/120/Tools/Binn/ManagementStudio/:/c/Tools/WebDriver:/c/Program Files (x86)/Microsoft SDKs/TypeScript/1.4/:/c/Program Files (x86)/Microsoft Visual Studio 12.0/Common7/IDE/PrivateAssemblies/:/c/Program Files (x86)/Microsoft SDKs/Azure/CLI/wbin:/c/Ruby193/bin:/c/Tools/NUnit/bin:/c/Tools/xUnit:/c/Tools/MSpec:/c/Tools/Coverity/bin:/c/Program Files (x86)/CMake/bin:/c/go/bin:/c/Program Files/Java/jdk1.8.0/bin:/c/Python27:/c/Program Files/nodejs:/c/Program Files (x86)/iojs:/c/Program Files/iojs:/c/Program Files/Microsoft SQL Server/130/Tools/Binn/:/c/Program Files (x86)/MSBuild/14.0/Bin:/c/Tools/NuGet:/c/Program Files (x86)/Microsoft Visual Studio 14.0/Common7/IDE/CommonExtensions/Microsoft/TestWindow:/c/Program Files/Microsoft DNX/Dnvm:/c/Program Files/Microsoft SQL Server/Client SDK/ODBC/130/Tools/Binn/:/c/Program Files (x86)/Microsoft SQL Server/130/Tools/Binn/:/c/Program Files (x86)/Microsoft SQL Server/130/DTS/Binn/:/c/Program Files/Microsoft SQL Server/130/DTS/Binn/:/c/Program Files (x86)/Microsoft SQL Server/110/DTS/Binn/:/c/Program Files (x86)/Microsoft SQL Server/120/DTS/Binn/:/c/Program Files (x86)/Apache/Maven/bin:/c/Python27/Scripts:/c/Tools/NUnit3:/c/Program Files/Mercurial/:/c/Program Files/dotnet/:/c/Tools/curl/bin:/c/Program Files/Amazon/AWSCLI/:/c/Program Files (x86)/Microsoft SQL Server/140/DTS/Binn/:/c/Program Files (x86)/Microsoft Visual Studio 14.0/Common7/IDE/Extensions/Microsoft/SQLDB/DAC/140:/c/Tools/vcpkg:/c/Program Files (x86)/Microsoft SQL Server/140/Tools/Binn/:/c/Program Files/Microsoft SQL Server/140/Tools/Binn/:/c/Program Files/Microsoft SQL Server/140/DTS/Binn/:/c/Program Files/erl9.2/bin:/c/Program Files (x86)/NSIS:/c/Tools/Octopus:/c/Program Files/Git/cmd:/c/Program Files/Git/usr/bin:/c/Program Files/Microsoft Service Fabric/bin/Fabric/Fabric.Code:/c/Program Files/Microsoft SDKs/Service Fabric/Tools/ServiceFabricLocalClusterManager:/c/Program Files/LLVM/bin:/c/Program Files (x86)/Yarn/bin/:/c/Users/appveyor/AppData/Roaming/npm:/c/Program Files/PowerShell/6/:/c/ProgramData/chocolatey/bin:/c/Program Files (x86)/nodejs/:/c/Users/appveyor/.dotnet/tools:/c/Users/appveyor/AppData/Local/Yarn/bin:/c/Users/appveyor/AppData/Roaming/npm:/c/Program Files/AppVeyor/BuildAgent/:/usr/texbin'
766+ R_BUILD_ARGS=--no-manual
767+ R_CHECK_ARGS='--no-manual --as-cran'
768+ R_VERSION_TEST='getRversion() >= '''3.5.0''''
769+ R_USE_BIOC_INST='source('''http://bioconductor.org/biocLite.R'''); tryCatch(useDevel(FALSE), error=function(e) {if (!grepl('''already in use''', e)) {e}}); options(repos=biocinstallRepos())'
770+ R_USE_BIOC_MNGR='if (!requireNamespace('''BiocManager''', quietly=TRUE)) install.packages('''BiocManager''', repos=c(CRAN='''https://cran.rstudio.com''')); if (FALSE) BiocManager::install(version = '''devel'''); options(repos=BiocManager::repositories())'
771+ R_USE_BIOC_CMDS='if (getRversion() >= '''3.5.0''') {if (!requireNamespace('''BiocManager''', quietly=TRUE)) install.packages('''BiocManager''', repos=c(CRAN='''https://cran.rstudio.com''')); if (FALSE) BiocManager::install(version = '''devel'''); options(repos=BiocManager::repositories())} else {source('''http://bioconductor.org/biocLite.R'''); tryCatch(useDevel(FALSE), error=function(e) {if (!grepl('''already in use''', e)) {e}}); options(repos=biocinstallRepos())};'
772+ BIOC_INSTALL='{if (getRversion() >= '''3.5.0''') BiocManager::install else BiocInstaller::biocLite}'
773+ COMMAND=install_deps
774+ echo 'Running command: install_deps'
775Running command: install_deps
776+ shift
777+ case $COMMAND in
778+ InstallDeps
779+ EnsureRemotes
780+ Rscript -e 'if (!("remotes" %in% rownames(installed.packages()))) q(status=1)'
781+ RBinaryInstall remotes
782+ [[ -z 1 ]]
783+ [[ Linux != \M\S\Y\S_\N\T-\6.\3-\W\O\W ]]
784+ echo 'Fallback: Installing from source'
785Fallback: Installing from source
786+ RInstall remotes
787+ [[ '' == \r\e\m\o\t\e\s ]]
788+ echo 'Installing R package(s): remotes'
789Installing R package(s): remotes
790+ Rscript -e 'install.packages(commandArgs(TRUE), repos="https://cran.rstudio.com", INSTALL_opts="", type="both")' remotes
791Installing package into 'c:/RLibrary'
792(as 'lib' is unspecified)
793trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/remotes_2.1.0.zip'
794Content type 'application/zip' length 355227 bytes (346 KB)
795==================================================
796downloaded 346 KB
797
798package 'remotes' successfully unpacked and MD5 sums checked
799
800The downloaded binary packages are in
801 C:\Users\appveyor\AppData\Local\Temp\1\RtmpWmcrju\downloaded_packages
802+ return
803+ Rscript -e 'if (!("remotes" %in% rownames(installed.packages()))) q(status=1)'
804+ Rscript -e 'options(repos=c(CRAN="https://cran.rstudio.com")); remotes::install_deps(dependencies = TRUE, type="both")'
805shiny (NA -> 1.3.2 ) [CRAN]
806shinydash... (NA -> 0.7.1 ) [CRAN]
807shinyjs (NA -> 1.0 ) [CRAN]
808rmarkdown (NA -> 1.13 ) [CRAN]
809htmltools (NA -> 0.3.6 ) [CRAN]
810highcharter (NA -> 0.7.0 ) [CRAN]
811tidyr (NA -> 0.8.3 ) [CRAN]
812dplyr (NA -> 0.8.2 ) [CRAN]
813purrr (NA -> 0.3.2 ) [CRAN]
814heatmaply (NA -> 0.16.0 ) [CRAN]
815plotly (NA -> 4.9.0 ) [CRAN]
816DT (NA -> 0.7 ) [CRAN]
817gplots (NA -> 3.0.1.1 ) [CRAN]
818dendextend (NA -> 1.12.0 ) [CRAN]
819htmlwidgets (NA -> 1.3 ) [CRAN]
820knitr (NA -> 1.23 ) [CRAN]
821httpuv (NA -> 1.5.1 ) [CRAN]
822mime (NA -> 0.7 ) [CRAN]
823jsonlite (NA -> 1.6 ) [CRAN]
824xtable (NA -> 1.8-4 ) [CRAN]
825sourcetools (NA -> 0.1.7 ) [CRAN]
826later (NA -> 0.8.0 ) [CRAN]
827promises (NA -> 1.0.1 ) [CRAN]
828yaml (NA -> 2.2.0 ) [CRAN]
829evaluate (NA -> 0.14 ) [CRAN]
830base64enc (NA -> 0.1-3 ) [CRAN]
831tinytex (NA -> 0.14 ) [CRAN]
832xfun (NA -> 0.8 ) [CRAN]
833rlist (NA -> 0.4.6.1 ) [CRAN]
834zoo (NA -> 1.8-6 ) [CRAN]
835broom (NA -> 0.5.2 ) [CRAN]
836xts (NA -> 0.11-2 ) [CRAN]
837quantmod (NA -> 0.4-15 ) [CRAN]
838igraph (NA -> 1.2.4.1 ) [CRAN]
839lubridate (NA -> 1.7.4 ) [CRAN]
840crosstalk (NA -> 1.0.0 ) [CRAN]
841whisker (NA -> 0.3-2 ) [CRAN]
842tidyselect (NA -> 0.2.5 ) [CRAN]
843plogr (NA -> 0.2.0 ) [CRAN]
844viridis (NA -> 0.5.1 ) [CRAN]
845seriation (NA -> 1.2-7 ) [CRAN]
846webshot (NA -> 0.5.1 ) [CRAN]
847httr (NA -> 1.4.0 ) [CRAN]
848hexbin (NA -> 1.27.3 ) [CRAN]
849data.table (NA -> 1.12.2 ) [CRAN]
850gtools (NA -> 3.8.1 ) [CRAN]
851gdata (NA -> 2.18.0 ) [CRAN]
852caTools (NA -> 1.17.1.2 ) [CRAN]
853highr (NA -> 0.8 ) [CRAN]
854markdown (NA -> 1.0 ) [CRAN]
855XML (NA -> 3.98-1.20) [CRAN]
856generics (NA -> 0.0.2 ) [CRAN]
857TTR (NA -> 0.23-4 ) [CRAN]
858curl (NA -> 3.3 ) [CRAN]
859openssl (NA -> 1.4 ) [CRAN]
860askpass (NA -> 1.1 ) [CRAN]
861sys (NA -> 3.2 ) [CRAN]
862gridExtra (NA -> 2.3 ) [CRAN]
863TSP (NA -> 1.1-7 ) [CRAN]
864qap (NA -> 0.1-1 ) [CRAN]
865gclus (NA -> 1.3.2 ) [CRAN]
866registry (NA -> 0.5-1 ) [CRAN]
867foreach (NA -> 1.4.4 ) [CRAN]
868iterators (NA -> 1.0.10 ) [CRAN]
869callr (NA -> 3.2.0 ) [CRAN]
870processx (NA -> 3.4.0 ) [CRAN]
871ps (NA -> 1.3.0 ) [CRAN]
872Skipping 4 packages not available: Biobase, MultiDataSet, GenomicRanges, BiocGenerics
873Installing 67 packages: shiny, shinydashboard, shinyjs, rmarkdown, htmltools, highcharter, tidyr, dplyr, purrr, heatmaply, plotly, DT, gplots, dendextend, htmlwidgets, knitr, httpuv, mime, jsonlite, xtable, sourcetools, later, promises, yaml, evaluate, base64enc, tinytex, xfun, rlist, zoo, broom, xts, quantmod, igraph, lubridate, crosstalk, whisker, tidyselect, plogr, viridis, seriation, webshot, httr, hexbin, data.table, gtools, gdata, caTools, highr, markdown, XML, generics, TTR, curl, openssl, askpass, sys, gridExtra, TSP, qap, gclus, registry, foreach, iterators, callr, processx, ps
874Installing packages into 'c:/RLibrary'
875(as 'lib' is unspecified)
876
877 There is a binary version available but the source version is later:
878 binary source needs_compilation
879processx 3.3.1 3.4.0 TRUE
880
881trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/shiny_1.3.2.zip'
882Content type 'application/zip' length 4694900 bytes (4.5 MB)
883==================================================
884downloaded 4.5 MB
885
886trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/shinydashboard_0.7.1.zip'
887Content type 'application/zip' length 332577 bytes (324 KB)
888==================================================
889downloaded 324 KB
890
891trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/shinyjs_1.0.zip'
892Content type 'application/zip' length 1036258 bytes (1011 KB)
893==================================================
894downloaded 1011 KB
895
896trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/rmarkdown_1.13.zip'
897Content type 'application/zip' length 3581886 bytes (3.4 MB)
898==================================================
899downloaded 3.4 MB
900
901trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/htmltools_0.3.6.zip'
902Content type 'application/zip' length 661102 bytes (645 KB)
903==================================================
904downloaded 645 KB
905
906trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/highcharter_0.7.0.zip'
907Content type 'application/zip' length 3002314 bytes (2.9 MB)
908==================================================
909downloaded 2.9 MB
910
911trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/tidyr_0.8.3.zip'
912Content type 'application/zip' length 955368 bytes (932 KB)
913==================================================
914downloaded 932 KB
915
916trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/dplyr_0.8.2.zip'
917Content type 'application/zip' length 3267184 bytes (3.1 MB)
918==================================================
919downloaded 3.1 MB
920
921trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/purrr_0.3.2.zip'
922Content type 'application/zip' length 421256 bytes (411 KB)
923==================================================
924downloaded 411 KB
925
926trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/heatmaply_0.16.0.zip'
927Content type 'application/zip' length 2063757 bytes (2.0 MB)
928==================================================
929downloaded 2.0 MB
930
931trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/plotly_4.9.0.zip'
932Content type 'application/zip' length 2849205 bytes (2.7 MB)
933==================================================
934downloaded 2.7 MB
935
936trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/DT_0.7.zip'
937Content type 'application/zip' length 1006111 bytes (982 KB)
938==================================================
939downloaded 982 KB
940
941trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/gplots_3.0.1.1.zip'
942Content type 'application/zip' length 659898 bytes (644 KB)
943==================================================
944downloaded 644 KB
945
946trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/dendextend_1.12.0.zip'
947Content type 'application/zip' length 2110738 bytes (2.0 MB)
948==================================================
949downloaded 2.0 MB
950
951trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/htmlwidgets_1.3.zip'
952Content type 'application/zip' length 806175 bytes (787 KB)
953==================================================
954downloaded 787 KB
955
956trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/knitr_1.23.zip'
957Content type 'application/zip' length 1420572 bytes (1.4 MB)
958==================================================
959downloaded 1.4 MB
960
961trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/httpuv_1.5.1.zip'
962Content type 'application/zip' length 1495307 bytes (1.4 MB)
963==================================================
964downloaded 1.4 MB
965
966trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/mime_0.7.zip'
967Content type 'application/zip' length 48231 bytes (47 KB)
968==================================================
969downloaded 47 KB
970
971trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/jsonlite_1.6.zip'
972Content type 'application/zip' length 1162330 bytes (1.1 MB)
973==================================================
974downloaded 1.1 MB
975
976trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/xtable_1.8-4.zip'
977Content type 'application/zip' length 706613 bytes (690 KB)
978==================================================
979downloaded 690 KB
980
981trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/sourcetools_0.1.7.zip'
982Content type 'application/zip' length 530712 bytes (518 KB)
983==================================================
984downloaded 518 KB
985
986trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/later_0.8.0.zip'
987Content type 'application/zip' length 611167 bytes (596 KB)
988==================================================
989downloaded 596 KB
990
991trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/promises_1.0.1.zip'
992Content type 'application/zip' length 696277 bytes (679 KB)
993==================================================
994downloaded 679 KB
995
996trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/yaml_2.2.0.zip'
997Content type 'application/zip' length 203889 bytes (199 KB)
998==================================================
999downloaded 199 KB
1000
1001trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/evaluate_0.14.zip'
1002Content type 'application/zip' length 76799 bytes (74 KB)
1003==================================================
1004downloaded 74 KB
1005
1006trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/base64enc_0.1-3.zip'
1007Content type 'application/zip' length 43488 bytes (42 KB)
1008==================================================
1009downloaded 42 KB
1010
1011trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/tinytex_0.14.zip'
1012Content type 'application/zip' length 98516 bytes (96 KB)
1013==================================================
1014downloaded 96 KB
1015
1016trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/xfun_0.8.zip'
1017Content type 'application/zip' length 173445 bytes (169 KB)
1018==================================================
1019downloaded 169 KB
1020
1021trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/rlist_0.4.6.1.zip'
1022Content type 'application/zip' length 236149 bytes (230 KB)
1023==================================================
1024downloaded 230 KB
1025
1026trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/zoo_1.8-6.zip'
1027Content type 'application/zip' length 1102598 bytes (1.1 MB)
1028==================================================
1029downloaded 1.1 MB
1030
1031trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/broom_0.5.2.zip'
1032Content type 'application/zip' length 2011890 bytes (1.9 MB)
1033==================================================
1034downloaded 1.9 MB
1035
1036trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/xts_0.11-2.zip'
1037Content type 'application/zip' length 963167 bytes (940 KB)
1038==================================================
1039downloaded 940 KB
1040
1041trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/quantmod_0.4-15.zip'
1042Content type 'application/zip' length 965470 bytes (942 KB)
1043==================================================
1044downloaded 942 KB
1045
1046trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/igraph_1.2.4.1.zip'
1047Content type 'application/zip' length 9183525 bytes (8.8 MB)
1048==================================================
1049downloaded 8.8 MB
1050
1051trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/lubridate_1.7.4.zip'
1052Content type 'application/zip' length 1577769 bytes (1.5 MB)
1053==================================================
1054downloaded 1.5 MB
1055
1056trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/crosstalk_1.0.0.zip'
1057Content type 'application/zip' length 665945 bytes (650 KB)
1058==================================================
1059downloaded 650 KB
1060
1061trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/whisker_0.3-2.zip'
1062Content type 'application/zip' length 81461 bytes (79 KB)
1063==================================================
1064downloaded 79 KB
1065
1066trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/tidyselect_0.2.5.zip'
1067Content type 'application/zip' length 626843 bytes (612 KB)
1068==================================================
1069downloaded 612 KB
1070
1071trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/plogr_0.2.0.zip'
1072Content type 'application/zip' length 18863 bytes (18 KB)
1073==================================================
1074downloaded 18 KB
1075
1076trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/viridis_0.5.1.zip'
1077Content type 'application/zip' length 1866766 bytes (1.8 MB)
1078==================================================
1079downloaded 1.8 MB
1080
1081trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/seriation_1.2-7.zip'
1082Content type 'application/zip' length 1218066 bytes (1.2 MB)
1083==================================================
1084downloaded 1.2 MB
1085
1086trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/webshot_0.5.1.zip'
1087Content type 'application/zip' length 141873 bytes (138 KB)
1088==================================================
1089downloaded 138 KB
1090
1091trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/httr_1.4.0.zip'
1092Content type 'application/zip' length 508435 bytes (496 KB)
1093==================================================
1094downloaded 496 KB
1095
1096trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/hexbin_1.27.3.zip'
1097Content type 'application/zip' length 936096 bytes (914 KB)
1098==================================================
1099downloaded 914 KB
1100
1101trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/data.table_1.12.2.zip'
1102Content type 'application/zip' length 1943894 bytes (1.9 MB)
1103==================================================
1104downloaded 1.9 MB
1105
1106trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/gtools_3.8.1.zip'
1107Content type 'application/zip' length 327154 bytes (319 KB)
1108==================================================
1109downloaded 319 KB
1110
1111trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/gdata_2.18.0.zip'
1112Content type 'application/zip' length 1264489 bytes (1.2 MB)
1113==================================================
1114downloaded 1.2 MB
1115
1116trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/caTools_1.17.1.2.zip'
1117Content type 'application/zip' length 330897 bytes (323 KB)
1118==================================================
1119downloaded 323 KB
1120
1121trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/highr_0.8.zip'
1122Content type 'application/zip' length 48750 bytes (47 KB)
1123==================================================
1124downloaded 47 KB
1125
1126trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/markdown_1.0.zip'
1127Content type 'application/zip' length 190087 bytes (185 KB)
1128==================================================
1129downloaded 185 KB
1130
1131trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/XML_3.98-1.20.zip'
1132Content type 'application/zip' length 4610084 bytes (4.4 MB)
1133==================================================
1134downloaded 4.4 MB
1135
1136trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/generics_0.0.2.zip'
1137Content type 'application/zip' length 64578 bytes (63 KB)
1138==================================================
1139downloaded 63 KB
1140
1141trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/TTR_0.23-4.zip'
1142Content type 'application/zip' length 525192 bytes (512 KB)
1143==================================================
1144downloaded 512 KB
1145
1146trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/curl_3.3.zip'
1147Content type 'application/zip' length 2996738 bytes (2.9 MB)
1148==================================================
1149downloaded 2.9 MB
1150
1151trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/openssl_1.4.zip'
1152Content type 'application/zip' length 3967028 bytes (3.8 MB)
1153==================================================
1154downloaded 3.8 MB
1155
1156trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/askpass_1.1.zip'
1157Content type 'application/zip' length 64664 bytes (63 KB)
1158==================================================
1159downloaded 63 KB
1160
1161trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/sys_3.2.zip'
1162Content type 'application/zip' length 59764 bytes (58 KB)
1163==================================================
1164downloaded 58 KB
1165
1166trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/gridExtra_2.3.zip'
1167Content type 'application/zip' length 1109356 bytes (1.1 MB)
1168==================================================
1169downloaded 1.1 MB
1170
1171trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/TSP_1.1-7.zip'
1172Content type 'application/zip' length 842432 bytes (822 KB)
1173==================================================
1174downloaded 822 KB
1175
1176trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/qap_0.1-1.zip'
1177Content type 'application/zip' length 537761 bytes (525 KB)
1178==================================================
1179downloaded 525 KB
1180
1181trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/gclus_1.3.2.zip'
1182Content type 'application/zip' length 416678 bytes (406 KB)
1183==================================================
1184downloaded 406 KB
1185
1186trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/registry_0.5-1.zip'
1187Content type 'application/zip' length 197133 bytes (192 KB)
1188==================================================
1189downloaded 192 KB
1190
1191trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/foreach_1.4.4.zip'
1192Content type 'application/zip' length 420060 bytes (410 KB)
1193==================================================
1194downloaded 410 KB
1195
1196trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/iterators_1.0.10.zip'
1197Content type 'application/zip' length 341871 bytes (333 KB)
1198==================================================
1199downloaded 333 KB
1200
1201trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/callr_3.2.0.zip'
1202Content type 'application/zip' length 257142 bytes (251 KB)
1203==================================================
1204downloaded 251 KB
1205
1206trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/ps_1.3.0.zip'
1207Content type 'application/zip' length 307674 bytes (300 KB)
1208==================================================
1209downloaded 300 KB
1210
1211package 'shiny' successfully unpacked and MD5 sums checked
1212package 'shinydashboard' successfully unpacked and MD5 sums checked
1213package 'shinyjs' successfully unpacked and MD5 sums checked
1214package 'rmarkdown' successfully unpacked and MD5 sums checked
1215package 'htmltools' successfully unpacked and MD5 sums checked
1216package 'highcharter' successfully unpacked and MD5 sums checked
1217package 'tidyr' successfully unpacked and MD5 sums checked
1218package 'dplyr' successfully unpacked and MD5 sums checked
1219package 'purrr' successfully unpacked and MD5 sums checked
1220package 'heatmaply' successfully unpacked and MD5 sums checked
1221package 'plotly' successfully unpacked and MD5 sums checked
1222package 'DT' successfully unpacked and MD5 sums checked
1223package 'gplots' successfully unpacked and MD5 sums checked
1224package 'dendextend' successfully unpacked and MD5 sums checked
1225package 'htmlwidgets' successfully unpacked and MD5 sums checked
1226package 'knitr' successfully unpacked and MD5 sums checked
1227package 'httpuv' successfully unpacked and MD5 sums checked
1228package 'mime' successfully unpacked and MD5 sums checked
1229package 'jsonlite' successfully unpacked and MD5 sums checked
1230package 'xtable' successfully unpacked and MD5 sums checked
1231package 'sourcetools' successfully unpacked and MD5 sums checked
1232package 'later' successfully unpacked and MD5 sums checked
1233package 'promises' successfully unpacked and MD5 sums checked
1234package 'yaml' successfully unpacked and MD5 sums checked
1235package 'evaluate' successfully unpacked and MD5 sums checked
1236package 'base64enc' successfully unpacked and MD5 sums checked
1237package 'tinytex' successfully unpacked and MD5 sums checked
1238package 'xfun' successfully unpacked and MD5 sums checked
1239package 'rlist' successfully unpacked and MD5 sums checked
1240package 'zoo' successfully unpacked and MD5 sums checked
1241package 'broom' successfully unpacked and MD5 sums checked
1242package 'xts' successfully unpacked and MD5 sums checked
1243package 'quantmod' successfully unpacked and MD5 sums checked
1244package 'igraph' successfully unpacked and MD5 sums checked
1245package 'lubridate' successfully unpacked and MD5 sums checked
1246package 'crosstalk' successfully unpacked and MD5 sums checked
1247package 'whisker' successfully unpacked and MD5 sums checked
1248package 'tidyselect' successfully unpacked and MD5 sums checked
1249package 'plogr' successfully unpacked and MD5 sums checked
1250package 'viridis' successfully unpacked and MD5 sums checked
1251package 'seriation' successfully unpacked and MD5 sums checked
1252package 'webshot' successfully unpacked and MD5 sums checked
1253package 'httr' successfully unpacked and MD5 sums checked
1254package 'hexbin' successfully unpacked and MD5 sums checked
1255package 'data.table' successfully unpacked and MD5 sums checked
1256package 'gtools' successfully unpacked and MD5 sums checked
1257package 'gdata' successfully unpacked and MD5 sums checked
1258package 'caTools' successfully unpacked and MD5 sums checked
1259package 'highr' successfully unpacked and MD5 sums checked
1260package 'markdown' successfully unpacked and MD5 sums checked
1261package 'XML' successfully unpacked and MD5 sums checked
1262package 'generics' successfully unpacked and MD5 sums checked
1263package 'TTR' successfully unpacked and MD5 sums checked
1264package 'curl' successfully unpacked and MD5 sums checked
1265package 'openssl' successfully unpacked and MD5 sums checked
1266package 'askpass' successfully unpacked and MD5 sums checked
1267package 'sys' successfully unpacked and MD5 sums checked
1268package 'gridExtra' successfully unpacked and MD5 sums checked
1269package 'TSP' successfully unpacked and MD5 sums checked
1270package 'qap' successfully unpacked and MD5 sums checked
1271package 'gclus' successfully unpacked and MD5 sums checked
1272package 'registry' successfully unpacked and MD5 sums checked
1273package 'foreach' successfully unpacked and MD5 sums checked
1274package 'iterators' successfully unpacked and MD5 sums checked
1275package 'callr' successfully unpacked and MD5 sums checked
1276package 'ps' successfully unpacked and MD5 sums checked
1277
1278The downloaded binary packages are in
1279 C:\Users\appveyor\AppData\Local\Temp\1\RtmpGEL39c\downloaded_packages
1280installing the source package 'processx'
1281
1282trying URL 'https://cran.rstudio.com/src/contrib/processx_3.4.0.tar.gz'
1283Content type 'application/x-gzip' length 123490 bytes (120 KB)
1284==================================================
1285downloaded 120 KB
1286
1287* installing source package 'processx' ...
1288** package 'processx' successfully unpacked and MD5 sums checked
1289** using staged installation
1290** libs
1291
1292*** arch - i386
1293C:/Rtools/mingw_32/bin/gcc -O3 -Wall -std=gnu99 -mtune=generic -Wall tools/px.c -o tools/px.exe
1294C:/Rtools/mingw_32/bin/gcc -O3 -Wall -std=gnu99 -mtune=generic -Wall tools/interrupt.c -o tools/interrupt.exe
1295C:/Rtools/mingw_32/bin/gcc -O3 -Wall -std=gnu99 -mtune=generic supervisor/supervisor.c supervisor/utils.c supervisor/windows.c -o supervisor/supervisor.exe
1296C:/Rtools/mingw_32/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O3 -Wall -std=gnu99 -mtune=generic -c init.c -o init.o
1297C:/Rtools/mingw_32/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O3 -Wall -std=gnu99 -mtune=generic -c poll.c -o poll.o
1298C:/Rtools/mingw_32/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O3 -Wall -std=gnu99 -mtune=generic -c errors.c -o errors.o
1299C:/Rtools/mingw_32/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O3 -Wall -std=gnu99 -mtune=generic -c processx-connection.c -o processx-connection.o
1300C:/Rtools/mingw_32/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O3 -Wall -std=gnu99 -mtune=generic -c processx-vector.c -o processx-vector.o
1301C:/Rtools/mingw_32/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O3 -Wall -std=gnu99 -mtune=generic -c create-time.c -o create-time.o
1302C:/Rtools/mingw_32/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O3 -Wall -std=gnu99 -mtune=generic -c base64.c -o base64.o
1303C:/Rtools/mingw_32/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O3 -Wall -std=gnu99 -mtune=generic -c win/processx.c -o win/processx.o
1304C:/Rtools/mingw_32/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O3 -Wall -std=gnu99 -mtune=generic -c win/stdio.c -o win/stdio.o
1305C:/Rtools/mingw_32/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O3 -Wall -std=gnu99 -mtune=generic -c win/named_pipe.c -o win/named_pipe.o
1306C:/Rtools/mingw_32/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O3 -Wall -std=gnu99 -mtune=generic -c win/utils.c -o win/utils.o
1307C:/Rtools/mingw_32/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O3 -Wall -std=gnu99 -mtune=generic -c win/thread.c -o win/thread.o
1308win/thread.c: In function 'processx__thread_getstatus_select':
1309win/thread.c:233:7: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
1310 int ret;
1311 ^
1312C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o processx.dll tmp.def init.o poll.o errors.o processx-connection.o processx-vector.o create-time.o base64.o win/processx.o win/stdio.o win/named_pipe.o win/utils.o win/thread.o -lws2_32 -Lc:/R/bin/i386 -lR
1313C:/Rtools/mingw_32/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O3 -Wall -std=gnu99 -mtune=generic -c client.c -o client.o
1314C:/Rtools/mingw_32/bin/gcc -Wl,--export-all-symbols -shared -o client.dll base64.o client.o errors.o -L"c:/R/bin/i386" -lR
1315installing via 'install.libs.R' to c:/RLibrary/00LOCK-processx/00new/processx
1316
1317*** arch - x64
1318C:/Rtools/mingw_64/bin/gcc -O2 -Wall -std=gnu99 -mtune=generic -Wall tools/px.c -o tools/px.exe
1319C:/Rtools/mingw_64/bin/gcc -O2 -Wall -std=gnu99 -mtune=generic -Wall tools/interrupt.c -o tools/interrupt.exe
1320C:/Rtools/mingw_64/bin/gcc -O2 -Wall -std=gnu99 -mtune=generic supervisor/supervisor.c supervisor/utils.c supervisor/windows.c -o supervisor/supervisor.exe
1321C:/Rtools/mingw_64/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O2 -Wall -std=gnu99 -mtune=generic -c init.c -o init.o
1322C:/Rtools/mingw_64/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O2 -Wall -std=gnu99 -mtune=generic -c poll.c -o poll.o
1323C:/Rtools/mingw_64/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O2 -Wall -std=gnu99 -mtune=generic -c errors.c -o errors.o
1324C:/Rtools/mingw_64/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O2 -Wall -std=gnu99 -mtune=generic -c processx-connection.c -o processx-connection.o
1325C:/Rtools/mingw_64/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O2 -Wall -std=gnu99 -mtune=generic -c processx-vector.c -o processx-vector.o
1326C:/Rtools/mingw_64/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O2 -Wall -std=gnu99 -mtune=generic -c create-time.c -o create-time.o
1327C:/Rtools/mingw_64/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O2 -Wall -std=gnu99 -mtune=generic -c base64.c -o base64.o
1328C:/Rtools/mingw_64/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O2 -Wall -std=gnu99 -mtune=generic -c win/processx.c -o win/processx.o
1329C:/Rtools/mingw_64/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O2 -Wall -std=gnu99 -mtune=generic -c win/stdio.c -o win/stdio.o
1330C:/Rtools/mingw_64/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O2 -Wall -std=gnu99 -mtune=generic -c win/named_pipe.c -o win/named_pipe.o
1331C:/Rtools/mingw_64/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O2 -Wall -std=gnu99 -mtune=generic -c win/utils.c -o win/utils.o
1332C:/Rtools/mingw_64/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O2 -Wall -std=gnu99 -mtune=generic -c win/thread.c -o win/thread.o
1333win/thread.c: In function 'processx__thread_getstatus_select':
1334win/thread.c:233:7: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
1335 int ret;
1336 ^
1337C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o processx.dll tmp.def init.o poll.o errors.o processx-connection.o processx-vector.o create-time.o base64.o win/processx.o win/stdio.o win/named_pipe.o win/utils.o win/thread.o -lws2_32 -Lc:/R/bin/x64 -lR
1338C:/Rtools/mingw_64/bin/gcc -I"c:/R/include" -DNDEBUG -DSTRICT_R_HEADERS -O2 -Wall -std=gnu99 -mtune=generic -c client.c -o client.o
1339C:/Rtools/mingw_64/bin/gcc -Wl,--export-all-symbols -shared -o client.dll base64.o client.o errors.o -L"c:/R/bin/x64" -lR
1340installing via 'install.libs.R' to c:/RLibrary/00LOCK-processx/00new/processx
1341** R
1342** inst
1343** byte-compile and prepare package for lazy loading
1344** help
1345*** installing help indices
1346 converting help for package 'processx'
1347 finding HTML links ... done
1348 base64_decode html
1349 curl_fds html
1350Rd warning: C:/Users/appveyor/AppData/Local/Temp/1/RtmpmoEK6j/R.INSTALL84823e2e1a/processx/man/curl_fds.Rd:11: file link 'multi_fdset' in package 'curl' does not exist and so has been treated as a topic
1351 default_pty_options html
1352 poll html
1353 process html
1354 process_initialize html
1355 processx_connections html
1356 run html
1357** building package indices
1358** testing if installed package can be loaded from temporary location
1359*** arch - i386
1360*** arch - x64
1361** testing if installed package can be loaded from final location
1362*** arch - i386
1363*** arch - x64
1364** testing if installed package keeps a record of temporary installation path
1365* DONE (processx)
1366
1367The downloaded source packages are in
1368 'C:\Users\appveyor\AppData\Local\Temp\1\RtmpGEL39c\downloaded_packages'
1369travis-tool.sh install_r htmltools httpuv evaluate
1370+ CRAN=https://cran.rstudio.com
1371+ BIOC=http://bioconductor.org/biocLite.R
1372+ PKGTYPE=both
1373+ BIOC_USE_DEVEL=FALSE
1374++ uname -s
1375+ OS=MSYS_NT-6.3-WOW
1376+ PANDOC_VERSION=1.13.1
1377+ PANDOC_DIR=/opt/pandoc
1378+ PANDOC_URL=https://s3.amazonaws.com/rstudio-buildtools/pandoc-1.13.1.zip
1379+ PATH='/c/Rtools/bin:/c/Rtools/MinGW/bin:/c/Rtools/gcc-4.6.3/bin:/c/R/bin/x64:/c/Rtools/mingw_64/bin:/usr/bin:/c/Program Files (x86)/Git/bin:/c/Program Files (x86)/Microsoft SDKs/Azure/CLI2/wbin:/c/Perl/site/bin:/c/Perl/bin:/c/Windows/system32:/c/Windows:/c/Windows/System32/Wbem:/c/Windows/System32/WindowsPowerShell/v1.0/:/c/Program Files/7-Zip:/c/Program Files/Microsoft/Web Platform Installer/:/c/Tools/GitVersion:/c/Tools/PsTools:/c/Program Files/Git LFS:/c/Program Files (x86)/Subversion/bin:/c/Program Files/Microsoft SQL Server/120/Tools/Binn/:/c/Program Files/Microsoft SQL Server/Client SDK/ODBC/110/Tools/Binn/:/c/Program Files (x86)/Microsoft SQL Server/120/Tools/Binn/:/c/Program Files/Microsoft SQL Server/120/DTS/Binn/:/c/Program Files (x86)/Microsoft SQL Server/120/Tools/Binn/ManagementStudio/:/c/Tools/WebDriver:/c/Program Files (x86)/Microsoft SDKs/TypeScript/1.4/:/c/Program Files (x86)/Microsoft Visual Studio 12.0/Common7/IDE/PrivateAssemblies/:/c/Program Files (x86)/Microsoft SDKs/Azure/CLI/wbin:/c/Ruby193/bin:/c/Tools/NUnit/bin:/c/Tools/xUnit:/c/Tools/MSpec:/c/Tools/Coverity/bin:/c/Program Files (x86)/CMake/bin:/c/go/bin:/c/Program Files/Java/jdk1.8.0/bin:/c/Python27:/c/Program Files/nodejs:/c/Program Files (x86)/iojs:/c/Program Files/iojs:/c/Program Files/Microsoft SQL Server/130/Tools/Binn/:/c/Program Files (x86)/MSBuild/14.0/Bin:/c/Tools/NuGet:/c/Program Files (x86)/Microsoft Visual Studio 14.0/Common7/IDE/CommonExtensions/Microsoft/TestWindow:/c/Program Files/Microsoft DNX/Dnvm:/c/Program Files/Microsoft SQL Server/Client SDK/ODBC/130/Tools/Binn/:/c/Program Files (x86)/Microsoft SQL Server/130/Tools/Binn/:/c/Program Files (x86)/Microsoft SQL Server/130/DTS/Binn/:/c/Program Files/Microsoft SQL Server/130/DTS/Binn/:/c/Program Files (x86)/Microsoft SQL Server/110/DTS/Binn/:/c/Program Files (x86)/Microsoft SQL Server/120/DTS/Binn/:/c/Program Files (x86)/Apache/Maven/bin:/c/Python27/Scripts:/c/Tools/NUnit3:/c/Program Files/Mercurial/:/c/Program Files/dotnet/:/c/Tools/curl/bin:/c/Program Files/Amazon/AWSCLI/:/c/Program Files (x86)/Microsoft SQL Server/140/DTS/Binn/:/c/Program Files (x86)/Microsoft Visual Studio 14.0/Common7/IDE/Extensions/Microsoft/SQLDB/DAC/140:/c/Tools/vcpkg:/c/Program Files (x86)/Microsoft SQL Server/140/Tools/Binn/:/c/Program Files/Microsoft SQL Server/140/Tools/Binn/:/c/Program Files/Microsoft SQL Server/140/DTS/Binn/:/c/Program Files/erl9.2/bin:/c/Program Files (x86)/NSIS:/c/Tools/Octopus:/c/Program Files/Git/cmd:/c/Program Files/Git/usr/bin:/c/Program Files/Microsoft Service Fabric/bin/Fabric/Fabric.Code:/c/Program Files/Microsoft SDKs/Service Fabric/Tools/ServiceFabricLocalClusterManager:/c/Program Files/LLVM/bin:/c/Program Files (x86)/Yarn/bin/:/c/Users/appveyor/AppData/Roaming/npm:/c/Program Files/PowerShell/6/:/c/ProgramData/chocolatey/bin:/c/Program Files (x86)/nodejs/:/c/Users/appveyor/.dotnet/tools:/c/Users/appveyor/AppData/Local/Yarn/bin:/c/Users/appveyor/AppData/Roaming/npm:/c/Program Files/AppVeyor/BuildAgent/:/usr/texbin'
1380+ R_BUILD_ARGS=--no-manual
1381+ R_CHECK_ARGS='--no-manual --as-cran'
1382+ R_VERSION_TEST='getRversion() >= '''3.5.0''''
1383+ R_USE_BIOC_INST='source('''http://bioconductor.org/biocLite.R'''); tryCatch(useDevel(FALSE), error=function(e) {if (!grepl('''already in use''', e)) {e}}); options(repos=biocinstallRepos())'
1384+ R_USE_BIOC_MNGR='if (!requireNamespace('''BiocManager''', quietly=TRUE)) install.packages('''BiocManager''', repos=c(CRAN='''https://cran.rstudio.com''')); if (FALSE) BiocManager::install(version = '''devel'''); options(repos=BiocManager::repositories())'
1385+ R_USE_BIOC_CMDS='if (getRversion() >= '''3.5.0''') {if (!requireNamespace('''BiocManager''', quietly=TRUE)) install.packages('''BiocManager''', repos=c(CRAN='''https://cran.rstudio.com''')); if (FALSE) BiocManager::install(version = '''devel'''); options(repos=BiocManager::repositories())} else {source('''http://bioconductor.org/biocLite.R'''); tryCatch(useDevel(FALSE), error=function(e) {if (!grepl('''already in use''', e)) {e}}); options(repos=biocinstallRepos())};'
1386+ BIOC_INSTALL='{if (getRversion() >= '''3.5.0''') BiocManager::install else BiocInstaller::biocLite}'
1387+ COMMAND=install_r
1388+ echo 'Running command: install_r'
1389Running command: install_r
1390+ shift
1391+ case $COMMAND in
1392+ RInstall htmltools httpuv evaluate
1393+ [[ '' == \h\t\m\l\t\o\o\l\s\ \h\t\t\p\u\v\ \e\v\a\l\u\a\t\e ]]
1394+ echo 'Installing R package(s): htmltools' httpuv evaluate
1395Installing R package(s): htmltools httpuv evaluate
1396+ Rscript -e 'install.packages(commandArgs(TRUE), repos="https://cran.rstudio.com", INSTALL_opts="", type="both")' htmltools httpuv evaluate
1397Installing packages into 'c:/RLibrary'
1398(as 'lib' is unspecified)
1399trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/htmltools_0.3.6.zip'
1400Content type 'application/zip' length 661102 bytes (645 KB)
1401==================================================
1402downloaded 645 KB
1403
1404trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/httpuv_1.5.1.zip'
1405Content type 'application/zip' length 1495307 bytes (1.4 MB)
1406==================================================
1407downloaded 1.4 MB
1408
1409trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/evaluate_0.14.zip'
1410Content type 'application/zip' length 76799 bytes (74 KB)
1411==================================================
1412downloaded 74 KB
1413
1414package 'htmltools' successfully unpacked and MD5 sums checked
1415package 'httpuv' successfully unpacked and MD5 sums checked
1416package 'evaluate' successfully unpacked and MD5 sums checked
1417
1418The downloaded binary packages are in
1419 C:\Users\appveyor\AppData\Local\Temp\1\RtmpQbFNGW\downloaded_packages
1420travis-tool.sh run_tests
1421+ CRAN=https://cran.rstudio.com
1422+ BIOC=http://bioconductor.org/biocLite.R
1423+ PKGTYPE=both
1424+ BIOC_USE_DEVEL=FALSE
1425++ uname -s
1426+ OS=MSYS_NT-6.3-WOW
1427+ PANDOC_VERSION=1.13.1
1428+ PANDOC_DIR=/opt/pandoc
1429+ PANDOC_URL=https://s3.amazonaws.com/rstudio-buildtools/pandoc-1.13.1.zip
1430+ PATH='/c/Rtools/bin:/c/Rtools/MinGW/bin:/c/Rtools/gcc-4.6.3/bin:/c/R/bin/x64:/c/Rtools/mingw_64/bin:/usr/bin:/c/Program Files (x86)/Git/bin:/c/Program Files (x86)/Microsoft SDKs/Azure/CLI2/wbin:/c/Perl/site/bin:/c/Perl/bin:/c/Windows/system32:/c/Windows:/c/Windows/System32/Wbem:/c/Windows/System32/WindowsPowerShell/v1.0/:/c/Program Files/7-Zip:/c/Program Files/Microsoft/Web Platform Installer/:/c/Tools/GitVersion:/c/Tools/PsTools:/c/Program Files/Git LFS:/c/Program Files (x86)/Subversion/bin:/c/Program Files/Microsoft SQL Server/120/Tools/Binn/:/c/Program Files/Microsoft SQL Server/Client SDK/ODBC/110/Tools/Binn/:/c/Program Files (x86)/Microsoft SQL Server/120/Tools/Binn/:/c/Program Files/Microsoft SQL Server/120/DTS/Binn/:/c/Program Files (x86)/Microsoft SQL Server/120/Tools/Binn/ManagementStudio/:/c/Tools/WebDriver:/c/Program Files (x86)/Microsoft SDKs/TypeScript/1.4/:/c/Program Files (x86)/Microsoft Visual Studio 12.0/Common7/IDE/PrivateAssemblies/:/c/Program Files (x86)/Microsoft SDKs/Azure/CLI/wbin:/c/Ruby193/bin:/c/Tools/NUnit/bin:/c/Tools/xUnit:/c/Tools/MSpec:/c/Tools/Coverity/bin:/c/Program Files (x86)/CMake/bin:/c/go/bin:/c/Program Files/Java/jdk1.8.0/bin:/c/Python27:/c/Program Files/nodejs:/c/Program Files (x86)/iojs:/c/Program Files/iojs:/c/Program Files/Microsoft SQL Server/130/Tools/Binn/:/c/Program Files (x86)/MSBuild/14.0/Bin:/c/Tools/NuGet:/c/Program Files (x86)/Microsoft Visual Studio 14.0/Common7/IDE/CommonExtensions/Microsoft/TestWindow:/c/Program Files/Microsoft DNX/Dnvm:/c/Program Files/Microsoft SQL Server/Client SDK/ODBC/130/Tools/Binn/:/c/Program Files (x86)/Microsoft SQL Server/130/Tools/Binn/:/c/Program Files (x86)/Microsoft SQL Server/130/DTS/Binn/:/c/Program Files/Microsoft SQL Server/130/DTS/Binn/:/c/Program Files (x86)/Microsoft SQL Server/110/DTS/Binn/:/c/Program Files (x86)/Microsoft SQL Server/120/DTS/Binn/:/c/Program Files (x86)/Apache/Maven/bin:/c/Python27/Scripts:/c/Tools/NUnit3:/c/Program Files/Mercurial/:/c/Program Files/dotnet/:/c/Tools/curl/bin:/c/Program Files/Amazon/AWSCLI/:/c/Program Files (x86)/Microsoft SQL Server/140/DTS/Binn/:/c/Program Files (x86)/Microsoft Visual Studio 14.0/Common7/IDE/Extensions/Microsoft/SQLDB/DAC/140:/c/Tools/vcpkg:/c/Program Files (x86)/Microsoft SQL Server/140/Tools/Binn/:/c/Program Files/Microsoft SQL Server/140/Tools/Binn/:/c/Program Files/Microsoft SQL Server/140/DTS/Binn/:/c/Program Files/erl9.2/bin:/c/Program Files (x86)/NSIS:/c/Tools/Octopus:/c/Program Files/Git/cmd:/c/Program Files/Git/usr/bin:/c/Program Files/Microsoft Service Fabric/bin/Fabric/Fabric.Code:/c/Program Files/Microsoft SDKs/Service Fabric/Tools/ServiceFabricLocalClusterManager:/c/Program Files/LLVM/bin:/c/Program Files (x86)/Yarn/bin/:/c/Users/appveyor/AppData/Roaming/npm:/c/Program Files/PowerShell/6/:/c/ProgramData/chocolatey/bin:/c/Program Files (x86)/nodejs/:/c/Users/appveyor/.dotnet/tools:/c/Users/appveyor/AppData/Local/Yarn/bin:/c/Users/appveyor/AppData/Roaming/npm:/c/Program Files/AppVeyor/BuildAgent/:/usr/texbin'
1431+ R_BUILD_ARGS=--no-manual
1432+ R_CHECK_ARGS='--no-manual --as-cran'
1433+ R_VERSION_TEST='getRversion() >= '''3.5.0''''
1434+ R_USE_BIOC_INST='source('''http://bioconductor.org/biocLite.R'''); tryCatch(useDevel(FALSE), error=function(e) {if (!grepl('''already in use''', e)) {e}}); options(repos=biocinstallRepos())'
1435+ R_USE_BIOC_MNGR='if (!requireNamespace('''BiocManager''', quietly=TRUE)) install.packages('''BiocManager''', repos=c(CRAN='''https://cran.rstudio.com''')); if (FALSE) BiocManager::install(version = '''devel'''); options(repos=BiocManager::repositories())'
1436+ R_USE_BIOC_CMDS='if (getRversion() >= '''3.5.0''') {if (!requireNamespace('''BiocManager''', quietly=TRUE)) install.packages('''BiocManager''', repos=c(CRAN='''https://cran.rstudio.com''')); if (FALSE) BiocManager::install(version = '''devel'''); options(repos=BiocManager::repositories())} else {source('''http://bioconductor.org/biocLite.R'''); tryCatch(useDevel(FALSE), error=function(e) {if (!grepl('''already in use''', e)) {e}}); options(repos=biocinstallRepos())};'
1437+ BIOC_INSTALL='{if (getRversion() >= '''3.5.0''') BiocManager::install else BiocInstaller::biocLite}'
1438+ COMMAND=run_tests
1439+ echo 'Running command: run_tests'
1440Running command: run_tests
1441+ shift
1442+ case $COMMAND in
1443+ RunTests
1444+ echo 'Building with: R CMD build --no-manual'
1445Building with: R CMD build --no-manual
1446+ [[ MSYS_ == \M\I\N\G\W ]]
1447+ [[ MSYS == \M\S\Y\S ]]
1448+ [[ -d vignettes ]]
1449+ rm -rf vignettes
1450+ Rscript -e 'd <- read.dcf('''DESCRIPTION'''); d[, colnames(d) == '''VignetteBuilder'''] <- NA; write.dcf(d, '''DESCRIPTION''')'
1451+ R CMD build --no-manual .
1452* checking for file './DESCRIPTION' ... OK
1453* preparing 'IntLIM':
1454* checking DESCRIPTION meta-information ... OK
1455* checking for LF line-endings in source and make files and shell scripts
1456* checking for empty or unneeded directories
1457* building 'IntLIM_0.1.0.tar.gz'
1458
1459++ ls -1t IntLIM_0.1.0.tar.gz
1460++ head -n 1
1461+ FILE=IntLIM_0.1.0.tar.gz
1462+ [[ MSYS_ == \M\I\N\G\W ]]
1463+ [[ MSYS == \M\S\Y\S ]]
1464+ R_CHECK_INSTALL_ARGS=--install-args=--build
1465+ echo 'Testing with: R CMD check "IntLIM_0.1.0.tar.gz" --no-manual --as-cran --install-args=--build'
1466Testing with: R CMD check "IntLIM_0.1.0.tar.gz" --no-manual --as-cran --install-args=--build
1467+ R_CHECK_CRAN_INCOMING=FALSE
1468+ [[ FALSE == \F\A\L\S\E ]]
1469+ echo '(CRAN incoming checks are off)'
1470(CRAN incoming checks are off)
1471+ R_CHECK_CRAN_INCOMING=FALSE
1472+ R_QPDF=true
1473+ R CMD check IntLIM_0.1.0.tar.gz --no-manual --as-cran --install-args=--build
1474* using log directory 'C:/projects/intlim/IntLIM.Rcheck'
1475* using R version 3.6.0 (2019-04-26)
1476* using platform: x86_64-w64-mingw32 (64-bit)
1477* using session charset: ISO8859-1
1478* using options '--no-manual --as-cran'
1479* checking for file 'IntLIM/DESCRIPTION' ... OK
1480* checking extension type ... Package
1481* this is package 'IntLIM' version '0.1.0'
1482* package encoding: UTF-8
1483* checking package namespace information ... OK
1484* checking package dependencies ... OK
1485* checking if this is a source package ... OK
1486* checking if there is a namespace ... OK
1487* checking for executable files ... OK
1488* checking for hidden files and directories ... NOTE
1489Found the following hidden files and directories:
1490 .appveyor.yml
1491These were most likely included in error. See section 'Package
1492structure' in the 'Writing R Extensions' manual.
1493* checking for portable file names ... OK
1494* checking serialization versions ... OK
1495* checking whether package 'IntLIM' can be installed ... OK
1496* checking installed package size ... NOTE
1497 installed size is 6.2Mb
1498 sub-directories of 1Mb or more:
1499 doc 5.4Mb
1500* checking package directory ... OK
1501* checking for future file timestamps ... OK
1502* checking DESCRIPTION meta-information ... OK
1503* checking top-level files ... OK
1504* checking for left-over files ... OK
1505* checking index information ... OK
1506* checking package subdirectories ... OK
1507* checking R files for non-ASCII characters ... OK
1508* checking R files for syntax errors ... OK
1509* checking whether the package can be loaded ... OK
1510* checking whether the package can be loaded with stated dependencies ... OK
1511* checking whether the package can be unloaded cleanly ... OK
1512* checking whether the namespace can be loaded with stated dependencies ... OK
1513* checking whether the namespace can be unloaded cleanly ... OK
1514* checking loading without being on the library search path ... OK
1515* checking dependencies in R code ... NOTE
1516There are ::: calls to the package's namespace in its code. A package
1517 almost never needs to use ::: for its own objects:
1518 'getCommon'
1519* checking S3 generic/method consistency ... OK
1520* checking replacement functions ... OK
1521* checking foreign function calls ... OK
1522* checking R code for possible problems ... OK
1523* checking Rd files ... OK
1524* checking Rd metadata ... OK
1525* checking Rd line widths ... OK
1526* checking Rd cross-references ... OK
1527* checking for missing documentation entries ... OK
1528* checking for code/documentation mismatches ... OK
1529* checking Rd \usage sections ... OK
1530* checking Rd contents ... OK
1531* checking for unstated dependencies in examples ... OK
1532* checking installed files from 'inst/doc' ... OK
1533* checking examples ...
This is a free service and has a 60 minutes time limit, see https://www.appveyor.com/pricing/
Hi Gaborcsardi,
I ran checks on windows machine, it took less than 5 min to check those examples. I have no clue on this ! Is this something related to AppVeyor ?
Thanks for help! -Rohith
Probably one of your examples freezes. Try to find which one, and then investigate why.