BioC 3.6: CHECK report for eiR on tokay1

Package: eiR

Version: 1.17.4

Command: rm -rf eiR.buildbin-libdir eiR.Rcheck && mkdir eiR.buildbin-libdir eiR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=eiR.buildbin-libdir eiR_1.17.4.tar.gz >eiR.Rcheck\00install.out 2>&1 && cp eiR.Rcheck\00install.out eiR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=eiR.buildbin-libdir --install="check:eiR-install.out" --force-multiarch --no-vignettes --timings eiR_1.17.4.tar.gz

StartedAt: 2017-10-17 22:03:17 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 22:11:10 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 473.1 seconds

RetCode: 1

Status:  ERROR

CheckDir: eiR.Rcheck

Warnings: NA

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### Running command:
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###   rm -rf eiR.buildbin-libdir eiR.Rcheck && mkdir eiR.buildbin-libdir eiR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=eiR.buildbin-libdir eiR_1.17.4.tar.gz >eiR.Rcheck\00install.out 2>&1 && cp eiR.Rcheck\00install.out eiR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=eiR.buildbin-libdir --install="check:eiR-install.out" --force-multiarch --no-vignettes --timings eiR_1.17.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/eiR.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'eiR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'eiR' version '1.17.4'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'eiR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'ChemmineR'
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  'BiocGenerics' 'RCurl' 'RUnit'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
insertEmbeddedDescriptors: no visible global function definition for
  'postgresqlWriteTable'
insertEmbeddedDescriptorsByCompoundId: no visible global function
  definition for 'postgresqlWriteTable'
insertGroupMembers: no visible global function definition for
  'postgresqlWriteTable'
Undefined global functions or variables:
  postgresqlWriteTable
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/eiR.buildbin-libdir/eiR/libs/i386/eiR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
eiAdd             3.87   1.58    7.83
eiPerformanceTest 3.55   1.50    5.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
eiAdd             6.33   1.83    8.41
eiQuery           4.72   1.92    6.70
eiCluster         4.61   1.70    6.60
eiPerformanceTest 4.14   1.82    6.28
eiMakeDb          2.98   1.92    5.05
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386/R" CMD BATCH --vanilla  "runTests.R" "runTests.Rout"' had status 1 
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
    no information found for 0
  
  Test files with failing tests
  
     test_main.R 
       test_bb.eiMakeDb 
       test_ca.eiQuery 
       test_da.eiPerformanceTest 
       test_ea.eiAdd 
       test_fa.eiCluster 
  
  
  Error in BiocGenerics:::testPackage("eiR") : 
    unit tests failed for package eiR
  Execution halted
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 6 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/eiR.Rcheck/00check.log'
for details.

R version 3.4.2 Patched (2017-10-07 r73498) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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

> BiocGenerics:::testPackage("eiR")
test_main start
Loading required package: RSQLite
[1] "createing db"
[1] "createing db"
eiInit tests
default descriptor
loaded 100 compounds
[1] "100  loaded by eiInit"
setting priorities for 4 groups.
fp descriptor
[1] "createing db"
using cluster
[1] 0
[1] "0  loaded by eiInit"
starting worker for localhost:11013 
starting worker for localhost:11013 
starting worker for localhost:11013 
[1] "set1"
  [1] 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218
 [19] 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236
 [37] 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254
 [55] 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272
 [73] 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290
 [91] 291 292 293 294 295 296 297 298 299 300
[1] "set2"
 [1] 201 202 205 208 209 210 211 217 218 219 220 223 224 225 226 229 231 233 234
[20] 236 238 243 245 246 247 248 249 251 253 266 267 270 271 272 273 274 275 277
[39] 278 279 280 281 282 283 287 288 289 291 299 300
Type: EXEC 
Type: EXEC 
Type: EXEC 
Type: EXEC 
Type: EXEC 
Type: EXEC 
Type: EXEC 
Type: EXEC 
Type: EXEC 
Type: EXEC 
Type: EXEC 
Type: EXEC 
Type: EXEC 
Type: EXEC 
Type: EXEC 
Type: EXEC 
Type: EXEC 
Type: EXEC 
evaluationg results
Type: EXEC 
in indexProcessor: 1
[1] "partFilename:  test_workspace/parDist.final.part-1"
starting
Loading required package: eiR
Loading required package: ChemmineR
Loading required package: DBI
Loading required package: RSQLite
in reduce
Type: DONE 
Type: DONE 
Type: DONE 
  eiMakeDb   
starting worker for localhost:11013 
[1] "by file name"
found 96 un-embedded descriptors for runId 1
Type: EXEC 
Type: EXEC 
Type: EXEC 
Type: EXEC 
Loading required package: eiR
Loading required package: ChemmineR
Loading required package: DBI
Loading required package: RSQLite
Regenerating matrix file...
Regenerating matrix file...
found 50 refs
found 10 samples
checking descriptors
[1] "by number"
found 96 un-embedded descriptors for runId 2
Type: EXEC 
Type: EXEC 
Type: EXEC 
Type: EXEC 
Regenerating matrix file...
Regenerating matrix file...
found 50 refs
found 20 samples
checking descriptors
[1] "52614449152, 52615498752, 52616546304, 52616546305, 52617594880, 52617594881, 52618645504, 52619700224, 52619708416, 52620740608, 52620742656, 52621789184, 52621789185, 52622853120, 52622853121, 53688190976, 53688190977, 53688192000, 53688192001, 53688192002, 53688193024, 53688193025, 53688193026, 53688193027, 53688193028, 53688206336, 53688206337, 53688207360, 53689239552, 53689239553, 53689239554, 53689239555, 53689239556, 53689239557, 53689239558, 53689240576, 53689240577, 53689241600, 53689241601, 53689241602, 53689247744, 53689247745, 53689247746, 53689247747, 53689247748, 53689255936, 53689255937, 53690288128, 53690288129, 53690288130, 53690288131, 53690288132, 53690288133, 53690290176, 53690290177, 53690290178, 53690290179, 53690296320, 53690296321, 53690303488, 53690303489, 53690303490, 53690303491, 53690304512, 53690304513, 53690304514, 53690304515, 53691336704, 53691336705, 53691336706, 53691336707, 53691336708, 53691336709, 53691338752, 53691338753, 53691338754, 53692385280, 53692385281, 53692385282, 53692385283, 53692386304, 53692393472, 53692400640, 53692400641, 53692400642, 53692400643, 53692401664, 53693433856, 53693434880, 53693434881, 53693435904, 53693449216, 53693449217, 53693449218, 53693449219, 53694482432, 53694482433, 53695546368, 53695546369, 54764032000, 54765086720, 54765094912, 54766129152, 54768239616, 54768239617, 55835682816, 55835682817, 55835691008, 55836725248, 55836738560, 55836738561, 55836739584, 55838835712, 55838835713, 62279190528, 62280238080, 62280238081, 69797479424, 69797480448, 69797480449"
 [1]  0.24650510 -0.50000000 -0.40239847 -0.50000000  0.17012839  0.50000000
 [7]  0.50000000 -0.26443742  0.42130043  0.07583856 -0.50000000  0.50000000
[13] -0.48964182  0.45011468 -0.21761118  0.50000000  0.50000000 -0.50000000
[19] -0.12295167  0.44697794 -0.06690009  0.50000000 -0.50000000  0.50000000
[25] -0.50000000 -0.38553682  0.50000000 -0.50000000  0.50000000  0.12874544
[31] -0.50000000  0.21017414 -0.50000000 -0.50000000 -0.19280440 -0.50000000
[37]  0.50000000 -0.50000000  0.50000000  0.50000000
 [1] -0.003122615  0.093823472 -0.010807548  0.126440477 -0.161177662
 [6]  0.003350615  0.160603826  0.019018220 -0.081853203 -0.086751499
[11] -0.075170248 -0.138982622  0.194434951  0.002663640 -0.131869420
[16]  0.031060396 -0.066437571 -0.268313517  0.168508805  0.071111218
[21] -0.293490463  0.147649121 -0.028886841  0.089898825 -0.138265391
[26]  0.071500557 -0.025291298  0.088078697 -0.102684228 -0.065708816
[31] -0.060223007  0.075751519  0.033600727  0.079275274  0.091291094
[36]  0.086621034  0.299698361 -0.062493072 -0.282590000 -0.056980149
Timing stopped at: 6.58 0.12 23.62
Error in checkDescriptor(conn, rid, descriptorIndex = i) : 
  descriptor mismatch found! db version does not match the just computed one
In addition: Warning message:
call dbDisconnect() when finished working with a connection 
Error in unserialize(node$con) : error reading from connection
Calls: local ... doTryCatch -> recvData -> recvData.SOCKnode -> unserialize
Execution halted
eiQuery
using runId 0
eiQuery test 1
Timing stopped at: 0.03 0.02 0.04
Error in eiQuery(runId, sdfsample[1:2], K = 15, asSimilarity = TRUE, dir = test_dir) : 
  no information found for 0
In addition: Warning message:
In .Internal(gc(verbose, reset)) :
  closing unused connection 3 (<-TOKAY1:11013)
Timing stopped at: 0 0 0
Error in eiPerformanceTest(runId, K = 22, dir = test_dir) : 
  no information found for 0
using runId 0
eiAdd test1
Timing stopped at: 0.35 0 0.34
Error in eiAdd(runId, examples[1:2], dir = test_dir) : 
  no information found for run 0
Timing stopped at: 0.01 0 0.01
Error in eiCluster(runId, K = numNbrs, minNbrs = minNbrs, cutoff = 1 -  : 
  no information found for 0


RUNIT TEST PROTOCOL -- Tue Oct 17 22:09:53 2017 
*********************************************** 
Number of test functions: 8 
Number of errors: 5 
Number of failures: 0 

 
1 Test Suite : 
eiR RUnit Tests - 8 test functions, 5 errors, 0 failures
ERROR in test_bb.eiMakeDb: Error in checkDescriptor(conn, rid, descriptorIndex = i) : 
  descriptor mismatch found! db version does not match the just computed one
ERROR in test_ca.eiQuery: Error in eiQuery(runId, sdfsample[1:2], K = 15, asSimilarity = TRUE, dir = test_dir) : 
  no information found for 0
ERROR in test_da.eiPerformanceTest: Error in eiPerformanceTest(runId, K = 22, dir = test_dir) : 
  no information found for 0
ERROR in test_ea.eiAdd: Error in eiAdd(runId, examples[1:2], dir = test_dir) : 
  no information found for run 0
ERROR in test_fa.eiCluster: Error in eiCluster(runId, K = numNbrs, minNbrs = minNbrs, cutoff = 1 -  : 
  no information found for 0

Test files with failing tests

   test_main.R 
     test_bb.eiMakeDb 
     test_ca.eiQuery 
     test_da.eiPerformanceTest 
     test_ea.eiAdd 
     test_fa.eiCluster 


Error in BiocGenerics:::testPackage("eiR") : 
  unit tests failed for package eiR
Execution halted

install for i386

* installing *source* package 'eiR' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c optimFunctions.cc -o optimFunctions.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o eiR.dll tmp.def optimFunctions.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/eiR.buildbin-libdir/eiR/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'eiR' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c optimFunctions.cc -o optimFunctions.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o eiR.dll tmp.def optimFunctions.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/eiR.buildbin-libdir/eiR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'eiR' as eiR_1.17.4.zip
* DONE (eiR)

name	user	system	elapsed
addTransform	0	0	0
eiAdd	3.87	1.58	7.83
eiCluster	2.92	1.55	4.53
eiInit	1.28	0.06	1.34
eiMakeDb	2.97	1.50	4.67
eiPerformanceTest	3.55	1.50	5.11
eiQuery	2.67	1.52	4.28
freeLSHData	0	0	0
loadLSHData	0	0	0
setDefaultDistance	0	0	0

name	user	system	elapsed
addTransform	0.02	0.00	0.02
eiAdd	6.33	1.83	8.41
eiCluster	4.61	1.70	6.60
eiInit	1.85	0.09	1.93
eiMakeDb	2.98	1.92	5.05
eiPerformanceTest	4.14	1.82	6.28
eiQuery	4.72	1.92	6.70
freeLSHData	0	0	0
loadLSHData	0	0	0
setDefaultDistance	0	0	0