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###
### Running command:
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### rm -rf rGADEM.buildbin-libdir && mkdir rGADEM.buildbin-libdir && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL --build --library=rGADEM.buildbin-libdir rGADEM_2.55.0.tar.gz
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* installing *source* package 'rGADEM' ...
** using staged installation
configure.win...
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Gadem_Analysis.c -o Gadem_Analysis.o
Gadem_Analysis.c: In function 'GADEM_Analysis':
Gadem_Analysis.c:274:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
274 | for (i=0; i<numSeq; i++) aveSeqLen +=seqLen[i]; aveSeqLen /=(double)numSeq;
| ^~~
Gadem_Analysis.c:274:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
274 | for (i=0; i<numSeq; i++) aveSeqLen +=seqLen[i]; aveSeqLen /=(double)numSeq;
| ^~~~~~~~~
Gadem_Analysis.c:182:59: warning: variable 'totalSitesInput' set but not used [-Wunused-but-set-variable]
182 | int cn[4],bcn[4],*seqCn,*bseqCn,avebnsites,avebnsiteSeq,totalSitesInput;
| ^~~~~~~~~~~~~~~
Gadem_Analysis.c:174:7: warning: variable 'generationNoMotif' set but not used [-Wunused-but-set-variable]
174 | int generationNoMotif; // maximal number of GA generations in a GADEM cycle resulted in no motifs
| ^~~~~~~~~~~~~~~~~
Gadem_Analysis.c:113:12: warning: variable 'logepwm' set but not used [-Wunused-but-set-variable]
113 | double **logepwm; // log(em-optimized PWM)
| ^~~~~~~
Gadem_Analysis.c: In function 'read_background':
Gadem_Analysis.c:1415:16: warning: zero-length gnu_printf format string [-Wformat-zero-length]
1415 | error("");
| ^~
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c align_sites.c -o align_sites.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c alloc.c -o alloc.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c background.c -o background.o
background.c: In function 'count_nucleotides':
background.c:818:10: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
818 | for (k=0; k<wordLen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
| ^~~
background.c:818:55: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
818 | for (k=0; k<wordLen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
| ^~
background.c:826:10: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
826 | for (k=0; k<wordLen; k++) s1[k]=rseq[i][j+k]; s1[k]='\0';
| ^~~
background.c:826:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
826 | for (k=0; k<wordLen; k++) s1[k]=rseq[i][j+k]; s1[k]='\0';
| ^~
background.c: In function 'll_score_backg_model':
background.c:1104:10: warning: variable 's1' set but not used [-Wunused-but-set-variable]
1104 | char *s1;
| ^~
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c base_frequency.c -o base_frequency.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c check_convergence.c -o check_convergence.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c check_pwm_dist.c -o check_pwm_dist.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c consensus.c -o consensus.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c construct_pwm.c -o construct_pwm.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c copy_pwm.c -o copy_pwm.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c crossover.c -o crossover.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c effect_seq_len.c -o effect_seq_len.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c evalue_meme.c -o evalue_meme.o
In file included from evalue_meme.c:61:
evalue_meme.c: In function 'llr_distr':
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
153 | error(""); \
| ^~
evalue_meme.c:155:3: note: in expansion of macro 'Resize'
155 | Resize(minI, N+1, int);
| ^~~~~~
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
153 | error(""); \
| ^~
evalue_meme.c:156:3: note: in expansion of macro 'Resize'
156 | Resize(maxI, N+1, int);
| ^~~~~~
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
153 | error(""); \
| ^~
evalue_meme.c:250:3: note: in expansion of macro 'Resize'
250 | Resize(prob, *range+2, double);
| ^~~~~~
evalue_meme.c: In function 'sum_distr':
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
153 | error(""); \
| ^~
evalue_meme.c:286:3: note: in expansion of macro 'Resize'
286 | Resize(d_sum, range+1, double); /* space for distribution */
| ^~~~~~
evalue_meme.c: In function 'cdf':
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
153 | error(""); \
| ^~
evalue_meme.c:325:3: note: in expansion of macro 'Resize'
325 | Resize(cdf, r+1, double);
| ^~~~~~
evalue_meme.c: In function 'get_llr_pv':
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
153 | error(""); \
| ^~
evalue_meme.c:393:5: note: in expansion of macro 'Resize'
393 | Resize(distrs, N+1, DISTR); /* create array of distributions */
| ^~~~~~
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
153 | error(""); \
| ^~
evalue_meme.c:410:5: note: in expansion of macro 'Resize'
410 | Resize(distrs[N].d, w+1, double *);
| ^~~~~~
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
153 | error(""); \
| ^~
evalue_meme.c:411:5: note: in expansion of macro 'Resize'
411 | Resize(distrs[N].cdf, w+1, double *);
| ^~~~~~
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
153 | error(""); \
| ^~
evalue_meme.c:412:5: note: in expansion of macro 'Resize'
412 | Resize(distrs[N].offset, w+1, int);
| ^~~~~~
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
153 | error(""); \
| ^~
evalue_meme.c:413:5: note: in expansion of macro 'Resize'
413 | Resize(distrs[N].range, w+1, int);
| ^~~~~~
evalue_meme.c: In function 'get_log_nalign':
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
153 | error(""); \
| ^~
evalue_meme.c:520:5: note: in expansion of macro 'Resize'
520 | Resize(len, nseqs, int);
| ^~~~~~
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c extend_alignment.c -o extend_alignment.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c initial_population.c -o initial_population.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mask_sites.c -o mask_sites.o
mask_sites.c: In function 'mask_repetitive':
mask_sites.c:61:7: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
61 | for (k=0,i=id+1; i<strlen(fileName); i++,k++) maskedFileName[k]=fileName[i]; maskedFileName[k]='\0';
| ^~~
mask_sites.c:61:84: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
61 | for (k=0,i=id+1; i<strlen(fileName); i++,k++) maskedFileName[k]=fileName[i]; maskedFileName[k]='\0';
| ^~~~~~~~~~~~~~
mask_sites.c:69:10: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
69 | for (k=0; k<klen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
| ^~~
mask_sites.c:69:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
69 | for (k=0; k<klen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
| ^~
mask_sites.c:82:16: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
82 | for (k=0; k<klen; k++) s1[k]=seq[i][j+k+pos]; s1[k]='\0';
| ^~~
mask_sites.c:82:62: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
82 | for (k=0; k<klen; k++) s1[k]=seq[i][j+k+pos]; s1[k]='\0';
| ^~
mask_sites.c:107:10: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
107 | for (k=0; k<klen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
| ^~~
mask_sites.c:107:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
107 | for (k=0; k<klen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
| ^~
mask_sites.c:125:16: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
125 | for (k=0; k<klen; k++) s1[k]=seq[i][j+k+pos]; s1[k]='\0';
| ^~~
mask_sites.c:125:62: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
125 | for (k=0; k<klen; k++) s1[k]=seq[i][j+k+pos]; s1[k]='\0';
| ^~
mask_sites.c:141:10: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
141 | for (k=0; k<klen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
| ^~~
mask_sites.c:141:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
141 | for (k=0; k<klen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
| ^~
mask_sites.c:150:16: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
150 | for (k=0; k<klen; k++) s1[k]=seq[i][j+k+pos]; s1[k]='\0';
| ^~~
mask_sites.c:150:62: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
150 | for (k=0; k<klen; k++) s1[k]=seq[i][j+k+pos]; s1[k]='\0';
| ^~
mask_sites.c:34:50: warning: variable 'cn' set but not used [-Wunused-but-set-variable]
34 | int maxNumKmer,maxKmerLen,klen,numKmer,pos,id,cn;
| ^~
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mutation.c -o mutation.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c normalization.c -o normalization.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c output.c -o output.o
output.c: In function 'print_bed':
output.c:11:10: warning: unused variable 'f1' [-Wunused-variable]
11 | FILE *f1;
| ^~
output.c: In function 'print_result_R':
output.c:257:10: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
257 | for (j=site[i].pos+pwmLen; j<min(site[i].pos+pwmLen+FLANKING_BASES,seqLen[site[i].seq]); j++)
| ^~~
output.c:260:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
260 | INTEGER(SeqIden)[increment_sequence]=site[i].seq+1;
| ^~~~~~~
output.c:326:27: warning: unused variable 'number' [-Wunused-variable]
326 | int number = id;
| ^~~~~~
output.c:324:29: warning: unused variable 'base' [-Wunused-variable]
324 | const char base[] = "m";
| ^~~~
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwm_score_distr.c -o pwm_score_distr.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_matrix.c -o read_matrix.o
read_matrix.c: In function 'read_initial_pwm':
read_matrix.c:22:8: warning: variable 'checkfscanf' set but not used [-Wunused-but-set-variable]
22 | int checkfscanf;
| ^~~~~~~~~~~
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_pwm0.c -o read_pwm0.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_seq.c -o read_seq.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c reverse_seq.c -o reverse_seq.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sample_wo_replacement.c -o sample_wo_replacement.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scan_sites.c -o scan_sites.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c score_subsequence.c -o score_subsequence.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c selection.c -o selection.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sort.c -o sort.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c top_kmers.c -o top_kmers.o
top_kmers.c: In function 'count_k_tuples':
top_kmers.c:332:10: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
332 | for (k=0; k<kmerLen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
| ^~~
top_kmers.c:332:57: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
332 | for (k=0; k<kmerLen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
| ^~
top_kmers.c:333:10: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
333 | for (k=0; k<kmerLen; k++) s2[k]=rseq[i][seqLen[i]-kmerLen-j+k]; s2[k]='\0';
| ^~~
top_kmers.c:333:76: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
333 | for (k=0; k<kmerLen; k++) s2[k]=rseq[i][seqLen[i]-kmerLen-j+k]; s2[k]='\0';
| ^~
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c transform_pwm.c -o transform_pwm.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c weights.c -o weights.o
gcc -shared -s -static-libgcc -o rGADEM.dll tmp.def Gadem_Analysis.o align_sites.o alloc.o background.o base_frequency.o check_convergence.o check_pwm_dist.o consensus.o construct_pwm.o copy_pwm.o crossover.o effect_seq_len.o evalue_meme.o extend_alignment.o initial_population.o mask_sites.o mutation.o normalization.o output.o pwm_score_distr.o read_matrix.o read_pwm0.o read_seq.o reverse_seq.o sample_wo_replacement.o scan_sites.o score_subsequence.o selection.o sort.o top_kmers.o transform_pwm.o weights.o -lws2_32 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/meat/rGADEM.buildbin-libdir/00LOCK-rGADEM/00new/rGADEM/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'rGADEM' as rGADEM_2.55.0.zip
* DONE (rGADEM)
