Four subroutines, filerr, daterr, moderr, and paperr, output error messages to the console, then terminate execution. Subroutine paperr also outputs its error messages to pap.out.
Subroutine filerr, called by programs preped (section III.1), descstat, (section III.2), prepap (section III.3), simul (section III.4), papdr (section III.5), and gpe (section III.6) reports errors in the files in opening, reading, or premature end of file. The error messages follow:
1. Error opening trip.dat.
2. Error reading trip.dat.
3. End of file on trip.dat.
4. Error opening order.dat.
5. Error reading order.dat.
6. End of file on order.dat.
7. Error opening header.dat.
8. Error reading header.dat.
9. End of file on header.dat.
10. Error opening phen.dat.
11. Error reading phen.dat.
12. End of file on phen.dat.
13. Error opening ascer.dat.
14. Error reading ascer.dat.
15. End of file on ascer.dat.
16. Error opening papin.dat.
17. Error reading papin.dat.
18. End of file on papin.dat.
19. Error opening freq.dat.
20. Error reading freq.dat.
21. End of file on freq.dat.
22. Error opening tran.dat.
23. Error reading tran.dat.
24. End of file on tran.dat.
25. Error opening dmlp.dat.
26. Error reading dmlp.dat.
27. End of file on dmlp.dat.
28. Error opening qmlp.dat.
29. Error reading qmlp.dat.
30. End of file on qmlp.dat.
31. Error opening wgen.dat.
32. Error reading wgen.dat.
33. End of file on wgen.dat.
34. Error opening popln.dat.
35. Error reading popln.dat.
36. End of file on popln.dat.
37. Error opening model.dat.
38. Error reading model.dat.
39. End of file on model.dat.
40. Error opening prob.dat.
41. Error reading prob.dat.
Subroutine daterr, called by programs preped (section III.1), descstat (section III.2), prepap (section III.3), simul (section III.4), papdr (section III.5), and gpe (section III.6) reports errors in either the pedigree structure or the amount of storage allocated for the data. The pedigree structure errors require correction of trip.dat (section II.1 and B.1). The storage errors require increasing the indicated parameter value in the include files and recompiling. The error messages follow:
42. The number of variables exceeds MDATA. Increase MDATA and recompile.
43. The number of individuals with phenotype data exceeds MINDPH. Increase MINDPH and recompile.
44. Individual own parent.
45. The number of pedigrees exceeds MPEDGR. Increase MPEDGR and recompile.
46. The number of triplets exceeds MTRIPS. Increase MTRIPS and recompile.
47. The number in the nuclear family exceeds MFAMEM. Increase MFAMEM and recompile.
48. The number of nuclear families in the sample exceeds MFAMTL. Increase MFAMTL and recompile.
49. The number of nuclear families in a pedigree exceeds MFAMPD. Increase MFAMPD and recompile.
50. The number of offspring requiring joint likelihoods exceeds MCHJT. Increase MCHJT and recompile.
51. The number in one pedigree exceeds MINDPD. Increase MINDPD and recompile.
52. The number of individuals exceeds MINDT. Increase MINDT and recompile.
53. The number of categories exceeds MCATEG. Increase MCATEG and recompile.
54. File trip.dat Has not been sorted.
55. Invalid ID number in trip.dat.
56. Individual duplicated in trip.dat.
57. Individual missing from trip.dat.
58. Individual occurs as an offspring more than once.
59. Family never used.
60. Pedigree missing from order.dat.
61. Marker missing allele count. Enter the number of alleles in header.dat.
62. NCOL and NDATA inconsistent. Correct header.dat.
63. The gender designation is incorrect for individual in phen.dat.
64. Individual has an invalid allele code. Correct phen.dat.
65. Too many variables for format statements. Split phen.dat into two files.
66. Marker phenotype allows all alleles. Genotype collapsing will not work.
67. Marker genotype corresponds to no phenotype. Correct popln.dat.
68. Marker genotype corresponds to more than one phenotype. Correct popln.dat.
69. Marker coded as autosomal in header.dat and X- linked in popln.dat.
70. Marker coded as X- linked in header.dat and autosomal in popln.dat.
71. The number of columns exceeds MCOL. Increase MCOL and recompile.
72. The standard deviation for variable equals zero. Correct header.dat.
73. Invalid code. Correct header.dat.
74. The number of spouses exceeds MSPOUSE. Increase MSPOUSE and recompile.
Subroutine moderr, called by descstat (section III.2), prepap (section III.3), simul (section III.4), and papdr (section III.5) reports errors in either the genetic model and parameter values or in the amount of storage allocated. Correct errors in the genetic model or parameter values by executing prepap. Correct errors in storage by increasing the parameter values in included file. The error messages follow:
75. The number of loci exceeds MLOCI. Increase MLOCI and recompile.
76. The number of variables included in the model exceeds MVAR. Increase MVAR and recompile.
77. The number of haplotypes exceeds MHAPTL. Increase MHAPTL and recompile.
78. The number of genotypes exceeds MGENTL. Increase MGENTL and recompile.
79. The number of variables included in the model exceeds MTRAIT. Increase MTRAIT and recompile.
80. The number of available subroutines exceeds MSUBRT. Increase MSUBRT and recompile.
81. The number of parameters required for the frequency exceeds MRFPR. Increase MFRPR and recompile.
82. The number of concomitant types required for the penetrance exceeds MCNTP. Increase MCNTP and recompile.
85. The number of frequency sets exceeds MFREQS. Increase MFREQS and recompile.
86. The number of values input for the frequencies exceeds MFREQT. Increase MFREQT and recompile.
87. The number of parameters for maximization, standard errors, or gridding exceeds MPARAM. Increase MPARAM and recompile.
88. The number of parameters held to the same value exceeds MPARSM. Increase MPARSM and recompile.
89. The number of linear constraints exceeds MCLIN. Increase MCLIN and recompile.
90. The number of markers included in the model exceeds MMARKR. Increase MMARKR and recompile.
91. Invalid genotype assignment code. Execute prepap to write model.dat correctly.
92. An X- linked locus is not allowed for the genotype assignment code selected. Execute prepap to write model.dat correctly.
93. Location of the marker in the variable list is less than 1 or greater than nvar. Execute prepap to write model.dat correctly.
94. Locus assigned for the marker is less than 1 or greater than NLOCI. Execute prepap to write model.dat correctly.
95. Location of the marker in phen.dat i less than 1 or greater than NDATA. Execute prepap to write model.dat correctly.
96. The frequency subroutine is inappropriate for the model as specified. Execute prepap to write model.dat correctly.
97. The transmission subroutine is inappropriate for the model as specified. Execute prepap to write model.dat correctly.
98. The major locus discrete subroutine is inappropriate for the model as specified. Execute prepap to write model.dat correctly.
99. The major locus quantitative subroutine is inappropriate for the model as specified. Execute prepap to write model.dat correctly.
100. The within genotype subroutine is inappropriate for the model as specified. Execute prepap to write model.dat correctly.
101. No frequency subroutines are available for the model as specified. Execute prepap to write model.dat correctly.
102. No transmission subroutines are available for the model as specified. Execute prepap to write model.dat correctly.
103. No major locus discrete subroutines are available for the model as specified. Execute prepap to write model.dat correctly.
104. No major locus quantitative subroutines are available for the model as specified. Execute prepap to write model.dat correctly.
105. No within genotype subroutines are available for the model as specified. Execute prepap to write model.dat correctly.
106. Location of the trait in the variable list is less than 1 or greater than nvar. Execute prepap to write model.dat correctly.
107. Trait has an invalid range of loci. Execute prepap to write model.dat correctly.
108. Values input for the penetrance parameter are too few or too many. Execute prepap to write model.dat correctly.
109. The mode of inheritance of the marker does not match the mode of inheritance of the locus. Execute prepap to write model.dat correctly.
110. The number of marker alleles in popln.dat incorrect. Execute prepap to write model.dat correctly.
111. The number of frequencies does not equal the number required for this model and subroutine. Execute prepap to write model.dat correctly.
112. Female recombination probability is incorrect. Execute prepap to write model.dat correctly.
113. Male recombination probability is incorrect. Execute prepap to write model.dat correctly.
114. Daughters transmission probability is incorrect. Execute prepap to write model.dat correctly.
115. Daughters transmission probability is less than zero or greater than one. Execute prepap to write model.dat correctly.
116. Sons transmission probability is incorrect. Execute prepap to write model.dat correctly.
117. Sons transmission probability is less than zero or greater than one. Execute prepap to write model.dat correctly.
118. Frequency count number is less than zero. Execute prepap to write model.dat correctly.
119. The number of trait genotypes exceeds MGTRAT. Increase MGTRAT and recompile.
120. Parameter is already being maximized.
121. The number of parameters required for the penetrance exceeds MPRTPD. Increase MPRTPD and recompile.
122. The number of parameters required for the penetrance exceeds MPRTPQ. Increase MPRTPQ and recompile.
123. The number of parameters required for the penetrance exceeds MPRTPW. Increase MPRTPW and recompile.
124. The number of penetrance parameters exceeds MPRD. Increase MPRD and recompile.
125. The number of penetrance parameters exceeds MPRQ. Increase MPRQ and recompile.
126. The number of penetrance parameters exceeds MPRW. Increase MPRW and recompile.
Subroutine paperr, called by simul (section III.4) and papdr (section III.5), reports execution errors. The errors include the linkage of subroutines inappropriate for model.dat, data and parameter values wrong for the subroutine, arrays too small for the data/genetic model combination, and execution errors. The error message follow:
127. The number of measurements exceeds MMEAS. Increase MMEAS and recompile.
128. The number of alleles for the marker exceeds MMKALL. Increase MMKALL and recompile.
129. The number of possible genotype combinations exceeds MADPH. Increase MADPH and recompile.
130. The number of stored likelihoods exceeds MPRLST. Increase MPRLST and recompile.
131. The frequency subroutine linked is not the one for which model.dat was written.
132. The transmission subroutine linked is not the one for which model.dat was written.
133. The major locus discrete subroutine linked is not the one for which model.dat was written.
134. The major locus quantitative subroutine linked is not the one for which model.dat was written.
135. The within genotype subroutine linked is not the one for which model.dat was written.
136. The penetrance subroutine linked is not the one for which model.dat was written.
137. The correlated penetrance subroutine linked is inappropriate for the penetrance subroutine.
138. This analysis must be performed using papdr.
139. Gender or other discrete categorization is missing for pedigree member.
140. Individual has an invalid disease code.
141. Individual has an age out of range.
142. Individual is missing age.
143. Individual is missing a covariate.
144. Marker phenotype for individual exceeds the number of phenotypes.
145. No marker genotypes possible for individual.
146. The prevalence is not increasing.
147. Parameter has maximized on the boundary.
148. Frequencies sum to more than one.
149. Correlation greater than one.
150. Too many tries to approximate the derivative.
151. The input value of parameter is not the maximum likelihood estimate.
152. The likelihood does not change with parameter.
153. The cutset size is larger than MCUTST. Increase MCUTST and recompile.)
154. The prevalence exceeds 1. Correct popln.dat.
155. The phenotype must be standardized to do a power transformation. Standardize in header.dat.
156. The number of genotypes possible for offspring exceeds MGENTP. Increase MGENTP and recompile.
157. The number of genotypes to comput probabilities for exceeds MGPRB. Increase MGPRB and recompile.
158. No genotypes possible for individual.
159. Correlations impossible for individual.
160. Assortative mating is restricted to autosomal inheritance.
161. Assortative mating is restricted to 3 or 6 genotypes.
162. File papin.dat is not appropriate for assortative mating. Rerun preped.
163. Assortative mating restricted to one trait.
164. Assortative mating requires that the means increase across genotypes.